Seed Endophytes Across Cultivars and Species, Associated Compositions, and Methods of Use Thereof

ABSTRACT

Materials and methods for improving plant traits and for providing plant fitness benefits are provided. In some embodiments, the materials, and methods employing the same, can comprise endophytes.

CROSS REFERENCE TO RELATED APPLICATIONS

This application is a continuation of U.S. application Ser. No.15/540,961, filed Jun. 29, 2018, allowed, which is the National Stage ofInternational Application No. PCT/US2015/068206, filed Dec. 30, 2015,which claims the benefit of and priority to International ApplicationNo. PCT/US2015/038187, filed Jun. 26, 2015, U.S. Provisional ApplicationNo. 62/156,021, filed May 1, 2015, U.S. Provisional Application No.62/156,028, filed May 1, 201 S, U.S. Provisional Application No.62/098,296, filed Dec. 30, 2014, U.S. Provisional Application No.62/098,298, filed Dec. 30, 2014, U.S. Provisional Application No.62/098,299, filed Dec. 30, 2014, U.S. Provisional Application No.62/098,302, filed Dec. 30, 2014, and U.S. Provisional Application No.62/098,304, filed Dec. 30, 2014, each of which is incorporated byreference it its entirety.

SEQUENCE LISTING

The instant application contains a Sequence Listing which has beensubmitted via EFS-Web and is hereby incorporated by reference in itsentirety. Said ASCII copy, created on Mar. 23, 2020, is named10035_Final_ST25.txt, and is 21,064,217 bytes in size.

FIELD OF THE INVENTION

Among other things, inventions disclosed herein relate to compositionsand methods for improving the cultivation of plants, particularlyagricultural plants. In an aspect, inventions described herein relate tobeneficial bacteria and fungi that are capable of living in a plant,which may be used to impart improved agronomic traits to the plants. Inanother aspect, inventions described herein relate to methods ofimproving plant characteristics by introducing synthetic combinations ofsuch beneficial bacteria and/or fungi to those plants. Further,inventions described herein also provide methods of treating seeds andother plant elements with synthetic combinations of beneficial bacteriaand/or fungi that are capable of living within a plant, to impartimproved agronomic characteristics to plants, particularly agriculturalplants.

BACKGROUND

Agriculture faces numerous challenges that are making it increasinglydifficult to provide food, materials, and fuels to the world'spopulation. Population growth and changes in diet associated with risingincomes are increasing global food demand, while many key resources foragriculture are becoming increasingly scarce. By 2050, the FAO projectsthat total food production must increase by 70% to meet the needs of thegrowing population, a challenge that is exacerbated by numerous factors,including diminishing freshwater resources, increasing competition forarable land, rising energy prices, increasing input costs, and thelikely need for crops to adapt to the pressures of a more extreme globalclimate. The need to grow nearly twice as much food in more uncertainclimates is driving a critical need for new innovations.

Today, crop performance is optimized via of technologies directedtowards the interplay between crop genotype (e.g., plant breeding,genetically-modified (GM) crops) and its surrounding environment (e.g.,fertilizer, synthetic herbicides, pesticides). While these paradigmshave assisted in doubling global food production in the past fiftyyears, yield growth rates have stalled in many major crops and shifts inthe climate have been linked to production declines in important cropssuch as wheat. In addition to their long development and regulatorytimelines, public fears of GM-crops and synthetic chemicals haschallenged their use in many key crops and countries, resulting in acomplete lack of acceptance for GM traits in wheat and the exclusion ofGM crops and many synthetic chemistries from European markets. Thus,there is a significant need for innovative, effective, andpublically-acceptable approaches to improving the intrinsic yield andresilience of crops to severe stresses.

SUMMARY OF THE INVENTION

The disclosures of PCT/US2014/044427, filed Jun. 26, 2014, U.S.application Ser. No. 14/316,469, filed Jun. 26, 2014, andPCT/US2014/054160, filed Sep. 4, 2014, are incorporated by reference intheir entirety, including the sequence listings containing SEQ ID NOs:1-1448.

The present invention is based on the discovery that a plant element(e.g., a whole plant, seedling, meristematic tissue, ground tissue,vascular tissue, dermal tissue, seed, leaf, root, shoot, stem, flower,fruit, stolon, bulb, tuber, corm, kelkis, shoot, bud) can be effectivelyaugmented by associating its surface with a single endophyte strain or aplurality of endophytes in an amount that is not normally found on theplant element. Endophytes described herein can be isolated from insidethe same plant or a different plant, or from inside a part or tissue ofthe same plant or different plant. The plant element thus associatedwith a single endophyte strain or a plurality of endophytes can be usedto confer improved agronomic trait or traits to the seed or the plantthat is grown or derived from the plant element.

In an embodiment, the invention features a method for improving anagricultural trait in an agricultural plant. In an embodiment, themethod includes providing an agricultural plant, seed or tissue thereof;contacting the plant, seed or tissue thereof with a formulationcomprising an endophyte that is common to at least two donor plant typesthat is present in the formulation in an amount effective to colonizethe plant; and growing the plants under conditions that allow theendophyte to improve a trait in the plant. In some embodiments, the twodonor plants are of the same family. In some embodiments, the two donorplants are of the same genus. In some embodiments, the two donor plantsare of the same species. In some embodiments, the agricultural planttissue is a seed. In a further embodiment, the population is disposed onthe surface of the seed.

In an embodiment, the method for improving an agricultural trait in anagricultural plant includes providing a modern agricultural plant, seedor tissue thereof; contacting the plant, seed, or tissue thereof with aformulation comprising an endophyte derived from an ancestral plant inan amount effective to colonize the plant; and allowing the plant togrow under conditions that allow the endophyte to colonize the plant.

The invention also features a method for preparing a seed comprising anendophyte population. The method comprising applying to an exteriorsurface of a seed a formulation comprising an endophyte populationconsisting essentially of an endophyte comprising a 16S rRNA or ITS rRNAnucleic acid sequence at least 95% identical to a nucleic acid sequenceselected from the group consisting of SEQ ID NOs: 1-455.

In some embodiments, provided herein is a method for treating seedlings.The method includes contacting foliage or the rhizosphere of a pluralityof agricultural plant seedlings with a seed a formulation comprising anendophyte population consisting essentially of an endophyte comprising a16S rRNA or ITS rRNA nucleic acid sequence at least 95% identical to anucleic acid sequence selected from the group consisting of SEQ ID NOs:1-455; and growing the contacted seedlings.

The invention also features a method for modulating a plant trait. Themethod includes applying to vegetation or an area adjacent thevegetation, a seed a formulation comprising an endophyte populationconsisting essentially of an endophyte comprising a 16S rRNA or ITS rRNAnucleic acid sequence at least 95% identical to a nucleic acid sequenceselected from the group consisting of SEQ ID NOs: 1-455, wherein theformulation is capable of providing a benefit to the vegetation, or to acrop produced from the vegetation.

A method for modulating a plant trait also is featured. The methodcomprising applying a formulation to soil, the seed a formulationcomprising an endophyte population consisting essentially of anendophyte comprising a 16S rRNA or ITS rRNA nucleic acid sequence atleast 95% identical to a nucleic acid sequence selected from the groupconsisting of SEQ ID NOs: 1-455, wherein the formulation is capable ofproviding a benefit to seeds planted within the soil, or to a cropproduced from plants grown in the soil.

In some embodiments, the endophyte comprises a 16S rRNA or ITS rRNAnucleic acid sequence at least 95% identical to a nucleic acid sequenceselected from the group consisting of SEQ ID NOs: 1-455. In someembodiments, the endophyte is capable of a function or activity selectedfrom the group consisting of auxin production, nitrogen fixation,production of an antimicrobial compound, mineral phosphatesolubilization, siderophore production, cellulase production, chitinaseproduction, xylanase production, and acetoin production. In someembodiments, the endophyte exhibits at least two of: auxin production,nitrogen fixation, production of an antimicrobial compound, mineralphosphate solubilization, siderophore production, cellulase production,chitinase production, xylanase production, and acetoin production.

In some embodiments, the endophyte is capable of metabolizing at leastone substrate selected from the group consisting of: a-D-glucose,arabinose, arbutin, b-methyl-D-galactoside, b-methyl-D-glucoside,D-alanine, D-arabitol, D-aspartic acid, D-cellobiose, dextrin,D-fructose, D-galactose, D-gluconic acid, D-glucosamine,dihydroxyacetone, DL-malic acid, D-mannitol, D-mannose, D-melezitose,D-melibiose, D-raffinose, D-ribose, D-serine, D-threonine, D-trehalose,D-xylose, g-amino-N-butyric acid, g-cyclodextrin, gelatin, gentiobiose,glycogen, glycyl-L-aspartic acid, glycyl-L-glutamic acid,glycyl-L-proline, glyoxylic acid, i-erythritol, inosine, L-alanine,L-alanyl-glycine, L-arabinose, L-asparagine, L-aspartic acid,L-galactonic acid-g-lactone, L-glutamic acid, L-glutamine, L-histidine,L-proline, L-rhamnose, L-serine, L-threonine, maltitol, maltose,maltotriose, mannose, N-acetyl-D-glucosamine, oxalic acid, palatinose,pectin, proline, salicin, stachyose, sucrose, trehalose, turanose,tyramine, uridine, and xylose.

In some embodiments, the endophyte is capable of metabolizing at leasttwo substrates selected from the group consisting of: a-D-glucose,arabinose, arbutin, b-methyl-D-galactoside, b-methyl-D-glucoside,D-alanine, D-arabitol, D-aspartic acid, D-cellobiose, dextrin,D-fructose, D-galactose, D-gluconic acid, D-glucosamine,dihydroxyacetone, DL-malic acid, D-mannitol, D-mannose, D-melezitose,D-melibiose, D-raffinose, D-ribose, D-serine, D-threonine, D-trehalose,D-xylose, g-amino-N-butyric acid, g-cyclodextrin, gelatin, gentiobiose,glycogen, glycyl-L-aspartic acid, glycyl-L-glutamic acid,glycyl-L-proline, glyoxylic acid, i-erythritol, inosine, L-alanine,L-alanyl-glycine, L-arabinose, L-asparagine, L-aspartic acid,L-galactonic acid-g-lactone, L-glutamic acid, L-glutamine, L-histidine,L-proline, L-rhamnose, L-serine, L-threonine, maltitol, maltose,maltotriose, mannose, N-acetyl-D-glucosamine, oxalic acid, palatinose,pectin, proline, salicin, stachyose, sucrose, trehalose, turanose,tyramine, uridine, and xylose.

In some embodiments, the endophyte is present at a concentration of atleast 10² CFU or spores per seed on the surface of seeds aftercontacting. In some embodiments, the applying or contacting comprisesspraying, immersing, coating, encapsulating, or dusting the seeds orseedlings with the formulation.

In some embodiments, the benefit or agricultural trait is selected fromthe group consisting of: increased root biomass, increased root length,increased height, increased shoot length, increased leaf number,increased water use efficiency, increased tolerance to low nitrogenstress, increased nitrogen use efficiency, increased overall biomass,increased grain yield, increased photosynthesis rate, increasedtolerance to drought, increased heat tolerance, increased salttolerance, increased resistance to nematode stress, increased resistanceto a fungal pathogen, increased resistance to a bacterial pathogen,increased resistance to a viral pathogen, a detectable modulation in thelevel of a metabolite, a detectable modulation in the transcriptome, anda detectable modulation in the proteome, relative to reference seeds oragricultural plants derived from reference seeds. In some embodiments,the benefit or agricultural trait comprises at least two benefits oragricultural traits selected from the group consisting of: increasedroot biomass, increased root length, increased height, increased shootlength, increased leaf number, increased water use efficiency, increasedtolerance to low nitrogen stress, increased nitrogen use efficiency,increased overall biomass, increased grain yield, increasedphotosynthesis rate, increased tolerance to drought, increased heattolerance, increased salt tolerance, increased resistance to nematodestress, increased resistance to a fungal pathogen, increased resistanceto a bacterial pathogen, increased resistance to a viral pathogen, adetectable modulation in the level of a metabolite, a detectablemodulation in the transcriptome, and a detectable modulation in theproteome, relative to reference seeds or agricultural plants derivedfrom reference seeds. In some embodiments, the benefit is increasedtolerance to low nitrogen stress or increased nitrogen use efficiency,and the endophyte is non-diazotrophic.

In some embodiments, the formulation comprises at least one memberselected from the group consisting of an agriculturally compatiblecarrier, a tackifier, a microbial stabilizer, a fungicide, anantibacterial agent, an herbicide, a nematicide, an insecticide, a plantgrowth regulator, a rodenticide, and a nutrient.

In some embodiments, the endophyte comprises a nucleic acid sequencethat is at least 97% identical to a nucleic acid sequence selected fromthe group consisting of SEQ ID NOs: 1-455, wherein the endophyte ispresent in the formulation in an amount effective to colonize the matureagricultural plant. In some embodiments, the endophyte comprises anucleic acid sequence that is at least 99% identical to a nucleic acidsequence selected from the group consisting of SEQ ID NOs: 1-455,wherein the endophyte is present in the formulation in an amounteffective to colonize the mature agricultural plant. In someembodiments, the endophyte comprises a nucleic acid sequence that is atleast 99.5% identical to a nucleic acid sequence selected from the groupconsisting of SEQ ID NOs: 1-455, wherein the endophyte is present in theformulation in an amount effective to colonize the mature agriculturalplant.

In some embodiments, the plant, seed or tissue thereof is contacted withat least 10 CFU or spores, at least 100 CFU or spores, at least 300 CFUor spores, at least 1,000 CFU or spores, at least 3,000 CFU or spores,at least 10,000 CFU or spores, at least 30,000 CFU or spores, at least100,000 CFU or spores, at least 300,000 CFU or spores, at least1,000,000 CFU or spores, or more, of the endophyte.

In some embodiments, the formulation comprises at least two endophytescomprising a nucleic acid sequence that is at least 97% identical, atleast 98% identical, at least 99% identical, at least 99.5% identical,or 100% identical, to a nucleic acid sequence selected from the groupconsisting of SEQ ID NOs: 1-455, wherein the at least two endophytes arepresent in the formulation in an amount effective to colonize the matureagricultural plant. In some embodiments, the formulation comprises atleast two endophytes provided in Table 1, Table 2, Table 7 and Table 8.

In some embodiments, the plant is a monocot. The monocot can be corn,wheat, barley or rice. In some embodiments, the plant is a dicot. Thedicot can be a soybean, peanut, canola, cotton, Brassica Napus, cabbage,lettuce, melon, strawberry, turnip, watermelon, tomato or pepper.

In some embodiments, the endophyte is present in the formulation in anamount effective to be detectable within a target tissue of theagricultural plant selected from a fruit, seed, leaf, root or portionthereof.

In some embodiments, the endophyte is detected in an amount of at least10 CFU or spores, at least 100 CFU or spores, at least 300 CFU orspores, at least 1,000 CFU or spores, at least 3,000 CFU or spores, atleast 10,000 CFU or spores, at least 30,000 CFU or spores, at least100,000 CFU or spores, at least 300,000 CFU or spores, at least1,000,000 CFU or spores, or more, in the target tissue.

In some embodiments, the endophyte is present in the formulation in anamount effective to increase the biomass and/or yield of the fruit orseed produced by the plant by at least 1%, at least 2%, at least 3%, atleast 5%, at least 10%, at least 15%, at least 20%, at least 30%, atleast 40%, at least 50%, at least 60%, at least 70%, at least 80%, atleast 90%, at least 100%, or more, when compared with the fruit or seedof a reference agricultural plant.

In some embodiments, the endophyte is present in the formulation in anamount effective to detectably increase the biomass of the plant ortissue thereof. In some embodiments, the biomass of the plant, or tissuethereof is detectably increased by at least 1%, at least 2%, at least3%, at least 5%, at least 10%, at least 15%, at least 20%, at least 30%,at least 40%, at least 50%, at least 60%, at least 70%, at least 80%, atleast 90%, at least 100%, or more, when compared with a referenceagricultural plant.

In some embodiments, the endophyte is present in the formulation in anamount effective to detectably increase the rate of germination of theseed. In some embodiments, the rate of germination of the seed isincreased by at least 0.5%, at least 1%, at least 2%, at least 3%, atleast 5%, at least 10%, at least 20%, at least 30%, at least 40%, atleast 50%, at least 60%, at least 70%, at least 80%, at least 90%, atleast 100% or more, when compared with a reference agricultural plant.

In some embodiments, the endophyte is present in the formulation in anamount effective to detectably induce production of auxin in the plant.In some embodiments, the production of auxin in the plant is increasedby at least 1%, at least 2%, at least 3%, at least 5%, at least 10%, atleast 20%, at least 30%, at least 40%, at least 50%, at least 60%, atleast 70%, at least 80%, at least 90%, at least 100% or more, whencompared with a reference agricultural plant.

The invention also features an agricultural plant, or portion of tissuethereof, comprising a formulation comprising an endophyte that is commonto at least two donor plant types that is disposed on an exteriorsurface of the plant or portion of tissue thereof, or within the plantor portion of tissue thereof, in an amount effective to colonize theplant, and in an amount effective to provide a benefit to the modernagricultural plant.

In some embodiments of the agricultural plant, or portion of tissuethereof, the endophyte comprises a nucleic acid sequence that is atleast 97% identical to a nucleic acid sequence selected from the groupconsisting of SEQ ID NOs: 1-455. In some embodiments of the agriculturalplant, or portion of tissue thereof, the endophyte comprises a nucleicacid sequence that is at least 99% identical to a nucleic acid sequenceselected from the group consisting of SEQ ID NOs: 1-455. In someembodiments of the agricultural plant, or portion of tissue thereof, theendophyte comprises a nucleic acid sequence that is at least 99.5%identical to a nucleic acid sequence selected from the group consistingof SEQ ID NOs: 1-455.

In some embodiments of the agricultural plant, or portion of tissuethereof, the endophyte is capable of a function or activity selectedfrom the group consisting of auxin production, nitrogen fixation,production of an antimicrobial compound, mineral phosphatesolubilization, siderophore production, cellulase production, chitinaseproduction, xylanase production, and acetoin production.

In some embodiments of the agricultural plant, or portion of tissuethereof, the endophyte exhibits at least two of: auxin production,nitrogen fixation, production of an antimicrobial compound, mineralphosphate solubilization, siderophore production, cellulase production,chitinase production, xylanase production, and acetoin production.

In some embodiments of the agricultural plant, or portion of tissuethereof, the endophyte is capable of metabolizing at least one substrateselected from the group consisting of: a-D-glucose, arabinose, arbutin,b-methyl-D-galactoside, b-methyl-D-glucoside, D-alanine, D-arabitol,D-aspartic acid, D-cellobiose, dextrin, D-fructose, D-galactose,D-gluconic acid, D-glucosamine, dihydroxyacetone, DL-malic acid,D-mannitol, D-mannose, D-melezitose, D-melibiose, D-raffinose, D-ribose,D-serine, D-threonine, D-trehalose, D-xylose, g-amino-N-butyric acid,g-cyclodextrin, gelatin, gentiobiose, glycogen, glycyl-L-aspartic acid,glycyl-L-glutamic acid, glycyl-L-proline, glyoxylic acid, i-erythritol,inosine, L-alanine, L-alanyl-glycine, L-arabinose, L-asparagine,L-aspartic acid, L-galactonic acid-g-lactone, L-glutamic acid,L-glutamine, L-histidine, L-proline, L-rhamnose, L-serine, L-threonine,maltitol, maltose, maltotriose, mannose, N-acetyl-D-glucosamine, oxalicacid, palatinose, pectin, proline, salicin, stachyose, sucrose,trehalose, turanose, tyramine, uridine, and xylose.

In some embodiments of the agricultural plant, or portion of tissuethereof, the endophyte is capable of metabolizing at least twosubstrates selected from the group consisting of: a-D-glucose,arabinose, arbutin, b-methyl-D-galactoside, b-methyl-D-glucoside,D-alanine, D-arabitol, D-aspartic acid, D-cellobiose, dextrin,D-fructose, D-galactose, D-gluconic acid, D-glucosamine,dihydroxyacetone, DL-malic acid, D-mannitol, D-mannose, D-melezitose,D-melibiose, D-raffinose, D-ribose, D-serine, D-threonine, D-trehalose,D-xylose, g-amino-N-butyric acid, g-cyclodextrin, gelatin, gentiobiose,glycogen, glycyl-L-aspartic acid, glycyl-L-glutamic acid,glycyl-L-proline, glyoxylic acid, i-erythritol, inosine, L-alanine,L-alanyl-glycine, L-arabinose, L-asparagine, L-aspartic acid,L-galactonic acid-g-lactone, L-glutamic acid, L-glutamine, L-histidine,L-proline, L-rhamnose, L-serine, L-threonine, maltitol, maltose,maltotriose, mannose, N-acetyl-D-glucosamine, oxalic acid, palatinose,pectin, proline, salicin, stachyose, sucrose, trehalose, turanose,tyramine, uridine, and xylose.

In some embodiments of the agricultural plant, or portion of tissuethereof, the formulation is disposed on an exterior surface of the plantor portion of tissue thereof, or within the plant or portion of tissuethereof, by spraying, immersing, coating, encapsulating, or dusting theplant or portion of tissue thereof with the formulation.

In some embodiments, the agricultural plant, or portion of tissuethereof further comprises a formulation that comprises at least onemember selected from the group consisting of an agriculturallycompatible carrier, a tackifier, a microbial stabilizer, a fungicide, anantibacterial agent, an herbicide, a nematicide, an insecticide, a plantgrowth regulator, a rodenticide, and a nutrient.

In some embodiments of the agricultural plant, or portion of tissuethereof, the benefit is selected from the group consisting of: increasedroot biomass, increased root length, increased height, increased shootlength, increased leaf number, increased water use efficiency, increasedtolerance to low nitrogen stress, increased nitrogen use efficiency,increased overall biomass, increased yield, increased photosynthesisrate, increased tolerance to drought, increased heat tolerance,increased salt tolerance, increased resistance to nematode stress,increased resistance to a fungal pathogen, increased resistance to abacterial pathogen, increased resistance to a viral pathogen, increasedresistance to herbivory, a detectable modulation in the level of ametabolite, a detectable modulation in the proteome, and a detectablemodulation in the transcriptome, relative to a reference agriculturalplant.

In some embodiments of the agricultural plant, or portion of tissuethereof, the benefit comprises at least two benefits selected from thegroup consisting of increased: root biomass, increased root length,increased height, increased shoot length, increased leaf number,increased water use efficiency, increased tolerance to low nitrogenstress, increased nitrogen use efficiency, increased overall biomass,increased yield, increased photosynthesis rate, increased tolerance todrought, increased heat tolerance, increased salt tolerance, increasedresistance to nematode stress, increased resistance to a fungalpathogen, increased resistance to a bacterial pathogen, increasedresistance to a viral pathogen, increased resistance to herbivory, adetectable modulation in the level of a metabolite, a detectablemodulation in the proteome, and a detectable modulation in thetranscriptome, relative to a reference agricultural plant. In someembodiments of the agricultural plant, or portion of tissue thereof, thebenefit is increased tolerance to low nitrogen stress or increasednitrogen use efficiency, and the endophyte is non-diazotrophic.

In some embodiments of the agricultural plant, or portion of tissuethereof, the plant or portion of tissue thereof is contacted with atleast 10 CFU or spores, at least 100 CFU or spores, at least 300 CFU orspores, at least 1,000 CFU or spores, at least 3,000 CFU or spores, atleast 10,000 CFU or spores, at least 30,000 CFU or spores, at least100,000 CFU or spores, at least 300,000 CFU or spores, at least1,000,000 CFU or spores, or more, of the endophyte. In some embodimentsof the agricultural plant, or portion of tissue thereof, the planttissue is a seed. In a further embodiment, the endophyte is disposed onthe surface of the seed.

In some embodiments, the agricultural plant, or portion of tissuethereof comprises at least two endophytes comprising a nucleic acidsequence that is at least 97% identical, at least 98% identical, atleast 99% identical, at least 99.5% identical, or 100% identical, to anucleic acid sequence selected from the group consisting of SEQ ID NOs:1-455 in an amount effective to colonize the mature agricultural plant.In some embodiments of the agricultural plant, or portion of tissuethereof, the two endophytes are selected from the groups disclosed inTable 1, Table 2, Table 7 and Table 8.

In some embodiments, the agricultural plant is a monocot. In someembodiments, the portion of tissue thereof is derived from a monocot.The monocot can be corn, wheat, barley or rice.

In some embodiments, the agricultural plant is a dicot. In someembodiments, the portion of tissue thereof is derived from a dicot. Thedicot can be a soybean, canola, cotton, Brassica Napus, tomato orpepper.

In some embodiments of the agricultural plant, or portion of tissuethereof, the endophyte is disposed in an amount effective to bedetectable within a target tissue of the mature target tissue of themature agricultural plant selected from a fruit, seed, leaf, root orportion thereof.

In some embodiments of the agricultural plant, or portion of tissuethereof, the population is disposed in an amount effective to increasethe rate of germination of the seed. The rate of germination of the seedcan be increased by at least 0.5%, at least 1%, at least 2%, at least3%, at least 5%, at least 10%, at least 20%, at least 30%, at least 40%,at least 50%, at least 60%, at least 70%, at least 80%, at least 90%, atleast 100% or more, when compared with a reference agricultural plant.

In some embodiments of the agricultural plant, or portion of tissuethereof, the population is disposed in an amount effective to bedetectable within a target tissue of the mature plant. The target tissuecan be the root, shoot, leaf, flower, fruit or seed.

In some embodiments of the agricultural plant, or portion of tissuethereof, the population is detected in an amount of at least 10 CFU orspores, at least 100 CFU or spores, at least 300 CFU or spores, at least1,000 CFU or spores, at least 3,000 CFU or spores, at least 10,000 CFUor spores, at least 30,000 CFU or spores, at least 100,000 CFU orspores, at least 300,000 CFU or spores, at least 1,000,000 CFU orspores, or more, in the plant or target tissue thereof.

In some embodiments of the agricultural plant, or portion of tissuethereof, the population of is disposed in an amount effective to bedetectable in the rhizosphere surrounding the plant. The population canbe detected in an amount of at least 10 CFU or spores, at least 100 CFUor spores, at least 300 CFU or spores, at least 1,000 CFU or spores, atleast 3,000 CFU or spores, at least 10,000 CFU or spores, at least30,000 CFU or spores, at least 100,000 CFU or spores, at least 300,000CFU or spores, at least 1,000,000 CFU or spores, or more, in therhizosphere surrounding the plant.

In some embodiments of the agricultural plant, or portion of tissuethereof, the population is disposed in an amount effective to detectablyincrease the biomass of the plant. The biomass of the plant can bedetectably increased by at least 1%, at least 2%, at least 3%, at least5%, at least 10%, at least 15%, at least 20%, at least 30%, at least40%, at least 50%, at least 60%, at least 70%, at least 80%, at least90%, at least 100%, or more, when compared with a reference agriculturalplant.

In some embodiments of the agricultural plant, or portion of tissuethereof, the population is disposed in an amount effective to increasethe biomass of a fruit or seed of the plant. The biomass of the fruit orseed of the plant can be detectably increased by at least 1%, at least2%, at least 3%, at least 5%, at least 10%, at least 15%, at least 20%,at least 30%, at least 40%, at least 50%, at least 60%, at least 70%, atleast 80%, at least 90%, at least 100%, or more, when compared with thefruit or seed of a reference agricultural plant.

In some embodiments of the agricultural plant, or portion of tissuethereof, the population is disposed in an amount effective to increasethe height of the plant. The height of the plant can be increased by atleast 1%, at least 2%, at least 3%, at least 5%, at least 10%, at least15%, at least 20%, at least 30%, at least 40%, at least 50%, at least60%, at least 70%, at least 80%, at least 90%, at least 100%, or more,when compared with the height of a reference agricultural plant.

In some embodiments of the agricultural plant, or portion of tissuethereof, the population is disposed in an amount effective to increaseproduction of auxin in the plant. The auxin production of the plant canbe increased by at least 1%, at least 2%, at least 3%, at least 5%, atleast 10%, at least 15%, at least 20%, at least 30%, at least 40%, atleast 50%, at least 60%, at least 70%, at least 80%, at least 90%, atleast 100%, or more, when compared with the auxin production of areference agricultural plant.

In some embodiments of the agricultural plant, or portion of tissuethereof, the population is disposed in an amount effective to increaseproduction of acetoin in the plant. The acetoin production of the plantcan be increased by at least 1%, at least 2%, at least 3%, at least 5%,at least 10%, at least 15%, at least 20%, at least 30%, at least 40%, atleast 50%, at least 60%, at least 70%, at least 80%, at least 90%, atleast 100%, or more, when compared with the acetoin production of areference agricultural plant.

In some embodiments of the agricultural plant, or portion of tissuethereof, the population is disposed in an amount effective to increaseproduction of siderophore in the plant. The siderophore production ofthe plant can be increased by at least 1%, at least 2%, at least 3%, atleast 5%, at least 10%, at least 15%, at least 20%, at least 30%, atleast 40%, at least 50%, at least 60%, at least 70%, at least 80%, atleast 90%, at least 100%, or more, when compared with the siderophoreproduction of a reference agricultural plant.

In some embodiments of the agricultural plant, or portion of tissuethereof, the population is disposed in an amount effective to increaseresistance to one or more stress conditions selected from the groupconsisting of a drought stress, heat stress, cold stress, salt stress,and low mineral stress.

In some embodiments of the agricultural plant, or portion of tissuethereof, the population is disposed in an amount effective to effectiveto increase resistance to one or more biotic stress conditions selectedfrom the group consisting of a nematode stress, insect herbivory stress,fungal pathogen stress, bacterial pathogen stress, and viral pathogenstress.

The invention also features bag comprising at least 1,000 seeds, whereineach seed comprises a formulation comprising an endophyte that is commonto at least two donor plant types that is disposed on an exteriorsurface of the plant or portion of tissue thereof, or within the plantor portion of tissue thereof, in an amount effective to colonize theplant, and in an amount effective to provide a benefit to the modernagricultural plant, wherein each seed is contacted with at least 10 CFUor spores, at least 100 CFU or spores, at least 300 CFU or spores, atleast 1,000 CFU or spores, at least 3,000 CFU or spores, at least 10,000CFU or spores, at least 30,000 CFU or spores, at least 100,000 CFU orspores, at least 300,000 CFU or spores, at least 1,000,000 CFU orspores, or more, of the endophyte, and wherein the bag further comprisesa label describing the seeds and/or the population.

In an embodiment, the invention features an agricultural formulationcomprising an endophyte comprising a nucleic acid sequence that is atleast 97% identical, at least 98% identical, at least 99% identical, atleast 99.5% identical, or 100% identical, to a nucleic acid sequenceselected from the group consisting of SEQ ID NOs: 1-455 that is presentin an amount effective to colonize a mature agricultural plant, whereinthe formulation further comprises at least one member selected from thegroup consisting of an agriculturally compatible carrier, a tackifier, amicrobial stabilizer, a fungicide, an antibacterial agent, an herbicide,a nematicide, an insecticide, a plant growth regulator, a rodenticide,and a nutrient.

In some embodiments of the agricultural formulation, the agriculturalplant is a monocot. The monocot can be maize, barley, rice, or wheat. Insome embodiments of the agricultural formulation, the agricultural plantis a dicot. The dicot can be soybean, canola, cotton, Brassica Napus,tomato, squash, cucumber, pepper, peanut, sunflower, or sugar beet.

In some embodiments of the agricultural formulation, the populationconsists essentially of an endophyte comprising a nucleic acid sequencethat is at least 99% identical to a nucleic acid sequence selected fromthe group consisting of SEQ ID NOs: 1-455. In some embodiments of theagricultural formulation, the population consists essentially of anendophyte comprising a nucleic acid sequence that is at least 99.5%identical to a nucleic acid sequence selected from the group consistingof SEQ ID NOs: 1-455.

The preparation of claim 87, comprising at least two differentendophytes each comprise a nucleic acid sequence that is at least 97%identical, at least 98% identical, at least 99% identical, at least99.5% identical, or 100% identical, to a nucleic acid sequence selectedfrom the group consisting of SEQ ID NOs: 1-455.

In some embodiments of the agricultural formulation, each of the twodifferent endophytes comprises the nucleic acid sequence disclosed inTable 1, Table 2, Table 7, and Table 8.

In some embodiments of the agricultural formulation, at least 1%, atleast 5%, at least 10%, at least 20%, at least 30%, at least 40%, atleast 50%, at least 75%, at least 80%, at least 90%, or at least 95% ormore, of the population is in spore form.

In some embodiments of the agricultural formulation, the endophytes wereadapted to culture on growth medium.

In some embodiments of the agricultural formulation, the preparation issubstantially stable at temperatures between about 0° C. and about 50°C. for at least three days. In some embodiments of the agriculturalformulation, the preparation is substantially stable at temperaturesbetween about 4° C. and about 37° C. for at least thirty days.

In some embodiments, the agricultural formulation is formulated toprovide a population of plants that demonstrates a substantiallyhomogenous growth rate when introduced into agricultural production.

The invention also features a method for making the plant comprising aformulation comprising an endophyte that is common to at least two donorplant types that is disposed on an exterior surface of the plant orportion of tissue thereof, or within the plant or portion of tissuethereof, in an amount effective to colonize the plant, and in an amounteffective to provide a benefit to the modern agricultural plant. Themethod includes providing a modern agricultural plant, and applying tothe plant a formulation comprising an endophyte comprising an endophyticmicrobe comprising a nucleic acid sequence that is at least 97%identical, at least 98% identical, at least 99% identical, at least99.5% identical, or 100% identical, to a nucleic acid sequence selectedfrom the group consisting of SEQ ID NOs: 1-455 that is present in anamount effective to colonize the plant.

The invention also features a commodity plant product comprising aplant, or a portion or part thereof, comprising a formulation comprisingan endophyte that is common to at least two donor plant types that isdisposed on an exterior surface of the plant or portion of tissuethereof, or within the plant or portion of tissue thereof, in an amounteffective to colonize the plant, and in an amount effective to provide abenefit to the modern agricultural plant. The commodity plant productcan be a grain, a flour, a starch, a syrup, a meal, an oil, a film, apackaging, a nutraceutical product, a pulp, an animal feed, a fishfodder, a bulk material for industrial chemicals, a cereal product, aprocessed human-food product, a sugar or an alcohol and protein.

The invention also features a method of producing a commodity plantproduct. The method includes obtaining a plant or plant tissue from aplant, progeny or derivative thereof, the plant comprising a formulationcomprising an endophyte that is common to at least two donor plant typesthat is disposed on an exterior surface of the plant or portion oftissue thereof, or within the plant or portion of tissue thereof, in anamount effective to colonize the plant, and in an amount effective toprovide a benefit to the modern agricultural plant; and producing thecommodity plant product therefrom.

The invention also features a synthetic combination comprising apurified microbial population in association with a plurality of seedsor seedlings of an agricultural plant, wherein the purified microbialpopulation comprises a first endophyte, wherein the first endophytecomprises a 16S rRNA or ITS rRNA nucleic acid sequence at least 97%identical to a nucleic acid sequence selected from the group consistingof SEQ ID NOs: 1-455, and wherein the endophyte is present in thesynthetic combination in an amount effective to provide a benefit to theseeds or seedlings or the plants derived from the seeds or seedlings.

In some embodiments of the synthetic combination comprising a purifiedmicrobial population, the first endophyte is capable of at least one of:production of an auxin, nitrogen fixation, production of anantimicrobial, production of a siderophore, mineral phosphatesolubilization, production of a cellulase, production of a chitinase,production of a xylanase, and production of acetoin, or a combination oftwo or more thereof.

In some embodiments of the synthetic combination comprising a purifiedmicrobial population, the microbial population further comprises asecond endophyte. In a further embodiment, the microbial populationcomprises a second microbial endophyte having an 16S rRNA or ITS rRNAnucleic acid sequence that is less than 95% identical to that of thefirst microbial endophyte.

In some embodiments of the synthetic combination comprising a purifiedmicrobial population, the microbial population further comprises asecond endophyte, and wherein the first and second endophytes areindependently capable of at least one of production of an auxin,nitrogen fixation, production of an antimicrobial, production of asiderophore, mineral phosphate solubilization, production of acellulase, production of a chitinase, production of a xylanase, orproduction of acetoin, or a combination of two or more thereof.

In some embodiments of the synthetic combination comprising a purifiedmicrobial population, the first and second endophytes are independentlycapable of at least one of production of an auxin, nitrogen fixation,production of an antimicrobial, production of a siderophore, mineralphosphate solubilization, production of a cellulase, production of achitinase, production of a xylanase, or production of acetoin, or acombination of two or more thereof.

In some embodiments of the synthetic combination comprising a purifiedmicrobial population, the microbial population further comprises asecond endophyte, wherein the first and second endophytes areindependently capable of metabolizing at least one substrate selectedfrom the group consisting of: a-D-glucose, arabinose, arbutin,b-methyl-D-galactoside, b-methyl-D-glucoside, D-alanine, D-arabitol,D-aspartic acid, D-cellobiose, dextrin, D-fructose, D-galactose,D-gluconic acid, D-glucosamine, dihydroxyacetone, DL-malic acid,D-mannitol, D-mannose, D-melezitose, D-melibiose, D-raffinose, D-ribose,D-serine, D-threonine, D-trehalose, D-xylose, g-amino-N-butyric acid,g-cyclodextrin, gelatin, gentiobiose, glycogen, glycyl-L-aspartic acid,glycyl-L-glutamic acid, glycyl-L-proline, glyoxylic acid, i-erythritol,inosine, L-alanine, L-alanyl-glycine, L-arabinose, L-asparagine,L-aspartic acid, L-galactonic acid-g-lactone, L-glutamic acid,L-glutamine, L-histidine, L-proline, L-rhamnose, L-serine, L-threonine,maltitol, maltose, maltotriose, mannose, N-acetyl-D-glucosamine, oxalicacid, palatinose, pectin, proline, salicin, stachyose, sucrose,trehalose, turanose, tyramine, uridine, and xylose, or a combination oftwo or more thereof.

The invention also features a synthetic combination comprising at leasttwo endophytes associated with a seed, wherein at least the firstendophyte is heterologous to the seed and wherein the first endophytecomprises a 16S rRNA or ITS rRNA nucleic acid sequence at least 97%identical to a nucleic acid sequence selected from the group consistingof SEQ ID NOs: 1-455, wherein the endophytes are present in theformulation in an amount effective to provide a benefit to the seeds orseedlings or the plants derived from the seeds or seedlings.

In some embodiments of the synthetic combination comprising at least twoendophytes, the second endophyte is a bacterial endophyte. In someembodiments of the synthetic combination comprising at least twoendophytes, the second endophyte is a fungal endophyte.

In some embodiments of the synthetic combination comprising at least twoendophytes, the first endophyte is a fungal endophyte. In someembodiments of the synthetic combination comprising at least twoendophytes, the first endophyte is a fungal endophyte and the secondendophyte is a fungal endophyte. In some embodiments of the syntheticcombination comprising at least two endophytes, the first endophyte is afungal endophyte and the second endophyte is a bacterial endophyte.

In some embodiments of the synthetic combination comprising at least twoendophytes, the first and second endophytes are independently capable ofmetabolizing at least one substrate selected from the group consistingof: a-D-glucose, arabinose, arbutin, b-methyl-D-galactoside,b-methyl-D-glucoside, D-alanine, D-arabitol, D-aspartic acid,D-cellobiose, dextrin, D-fructose, D-galactose, D-gluconic acid,D-glucosamine, dihydroxyacetone, DL-malic acid, D-mannitol, D-mannose,D-melezitose, D-melibiose, D-raffinose, D-ribose, D-serine, D-threonine,D-trehalose, D-xylose, g-amino-N-butyric acid, g-cyclodextrin, gelatin,gentiobiose, glycogen, glycyl-L-aspartic acid, glycyl-L-glutamic acid,glycyl-L-proline, glyoxylic acid, i-erythritol, inosine, L-alanine,L-alanyl-glycine, L-arabinose, L-asparagine, L-aspartic acid,L-galactonic acid-g-lactone, L-glutamic acid, L-glutamine, L-histidine,L-proline, L-rhamnose, L-serine, L-threonine, maltitol, maltose,maltotriose, mannose, N-acetyl-D-glucosamine, oxalic acid, palatinose,pectin, proline, salicin, stachyose, sucrose, trehalose, turanose,tyramine, uridine, and xylose, or a combination of two or more thereof.

In some embodiments of any of the synthetic combinations, the firstendophyte is capable of metabolizing at least one substrate selectedfrom the group of: a-D-glucose, arabinose, arbutin,b-methyl-D-galactoside, b-methyl-D-glucoside, D-alanine, D-arabitol,D-aspartic acid, D-cellobiose, dextrin, D-fructose, D-galactose,D-gluconic acid, D-glucosamine, dihydroxyacetone, DL-malic acid,D-mannitol, D-mannose, D-melezitose, D-melibiose, D-raffinose, D-ribose,D-serine, D-threonine, D-trehalose, D-xylose, g-amino-N-butyric acid,g-cyclodextrin, gelatin, gentiobiose, glycogen, glycyl-L-aspartic acid,glycyl-L-glutamic acid, glycyl-L-proline, glyoxylic acid, i-erythritol,inosine, L-alanine, L-alanyl-glycine, L-arabinose, L-asparagine,L-aspartic acid, L-galactonic acid-g-lactone, L-glutamic acid,L-glutamine, L-histidine, L-proline, L-rhamnose, L-serine, L-threonine,maltitol, maltose, maltotriose, mannose, N-acetyl-D-glucosamine, oxalicacid, palatinose, pectin, proline, salicin, stachyose, sucrose,trehalose, turanose, tyramine, uridine, and xylose. In some embodimentsof the synthetic combination comprising at least two endophytesassociated with a seed, both of the endophytes are heterologous to theseed.

In some embodiments of any of the synthetic combinations, the syntheticcombination is disposed within a packaging material selected from a bag,box, bin, envelope, carton, or container. In an embodiment of any of thesynthetic combinations, the synthetic combination comprises 1000 seedweight amount of seeds, wherein the packaging material optionallycomprises a desiccant, and wherein the synthetic combination optionallycomprises an anti-fungal agent.

In some embodiments of any of the synthetic combinations, the firstendophyte is localized on the surface of the seeds or seedlings. In someembodiments of any of the synthetic combinations, the first endophyte isobtained from a plant species other than the seeds or seedlings of thesynthetic combination. In some embodiments of any of the syntheticcombinations, the first endophyte is obtained from a plant cultivardifferent from the cultivar of the seeds or seedlings of the syntheticcombination. In some embodiments of any of the synthetic combinations,the first endophyte is obtained from a plant cultivar that is the sameas the cultivar of the seeds or seedlings of the synthetic combination.

In some embodiments of any of the synthetic combinations, the firstendophyte is a bacterial endophyte.

In some embodiments of any of the synthetic combinations, the firstendophyte is capable of at least two of auxin production, nitrogenfixation, production of an antimicrobial compound, mineral phosphatesolubilization, siderophore production, cellulase production, chitinaseproduction, xylanase production, and acetoin production.

In some embodiments of any of the synthetic combinations, the firstendophyte is capable of metabolizing at least two substrates selectedfrom the group consisting of: a-D-glucose, arabinose, arbutin,b-methyl-D-galactoside, b-methyl-D-glucoside, D-alanine, D-arabitol,D-aspartic acid, D-cellobiose, dextrin, D-fructose, D-galactose,D-gluconic acid, D-glucosamine, dihydroxyacetone, DL-malic acid,D-mannitol, D-mannose, D-melezitose, D-melibiose, D-raffinose, D-ribose,D-serine, D-threonine, D-trehalose, D-xylose, g-amino-N-butyric acid,g-cyclodextrin, gelatin, gentiobiose, glycogen, glycyl-L-aspartic acid,glycyl-L-glutamic acid, glycyl-L-proline, glyoxylic acid, i-erythritol,inosine, L-alanine, L-alanyl-glycine, L-arabinose, L-asparagine,L-aspartic acid, L-galactonic acid-g-lactone, L-glutamic acid,L-glutamine, L-histidine, L-proline, L-rhamnose, L-serine, L-threonine,maltitol, maltose, maltotriose, mannose, N-acetyl-D-glucosamine, oxalicacid, palatinose, pectin, proline, salicin, stachyose, sucrose,trehalose, turanose, tyramine, uridine, and xylose.

In some embodiments of any of the synthetic combinations, the benefit isselected from the group consisting of: increased root biomass, increasedroot length, increased height, increased shoot length, increased leafnumber, increased water use efficiency, increased tolerance to lownitrogen stress, increased nitrogen use efficiency, increased overallbiomass, increased grain yield, increased photosynthesis rate, increasedtolerance to drought, increased heat tolerance, increased salttolerance, increased resistance to nematode stress, increased resistanceto a fungal pathogen, increased resistance to a bacterial pathogen,increased resistance to a viral pathogen, a detectable modulation in thelevel of a metabolite, a detectable modulation in the transcriptome, anda detectable modulation in the proteome, relative to reference seeds oragricultural plants derived from reference seeds. In some embodiments,the benefit comprises at least two benefits selected from the groupconsisting of: increased root biomass, increased root length, increasedheight, increased shoot length, increased leaf number, increased wateruse efficiency, increased tolerance to low nitrogen stress, increasednitrogen use efficiency, increased overall biomass, increased grainyield, increased photosynthesis rate, increased tolerance to drought,increased heat tolerance, increased salt tolerance, increased resistanceto nematode stress, increased resistance to a fungal pathogen, increasedresistance to a bacterial pathogen, increased resistance to a viralpathogen, a detectable modulation in the level of a metabolite, adetectable modulation in the transcriptome, and a detectable modulationin the proteome, relative to reference seeds or agricultural plantsderived from reference seeds.

In some embodiments of any of the synthetic combinations, thecombination comprises seeds and the first endophyte is associated withthe seeds as a coating on the surface of the seeds. In some embodimentsof any of the synthetic combinations, the combination comprisesseedlings and the first endophyte is contacted with the seedlings as aspray applied to one or more leaves and/or one or more roots of theseedlings. In some embodiments of any of the synthetic combinations, thesynthetic combination further comprises one or more additional endophytespecies.

In some embodiments of any of the synthetic combinations, the effectiveamount is at least 1×102 CFU or spores/per seed. In some embodiments ofany of the synthetic combinations, the effective amount is at least1×103 CFU or spores/per seed. In some embodiments of any of thesynthetic combinations, the combination comprises seeds and theeffective amount is from about 1×102 CFU or spores/per seed to about1×108 CFU or spores/per seed.

In some embodiments of any of the synthetic combinations, the seed is aseed from an agricultural plant. In some embodiments of any of thesynthetic combinations, the seed is a transgenic seed.

In some embodiments of any of the synthetic combinations, the firstendophytes are present in an amount of at least 10 CFU or spores, atleast 100 CFU or spores, at least 300 CFU or spores, at least 1,000 CFUor spores, at least 3,000 CFU or spores, at least 10,000 CFU or spores,at least 30,000 CFU or spores, at least 100,000 CFU or spores, at least300,000 CFU or spores, or at least 1,000,000 CFU spores per seed.

In some embodiments, any of the synthetic combinations further compriseone or more of the following: a stabilizer, or a preservative, or acarrier, or a surfactant, an anticomplex agent, or any combinationthereof. In some embodiments, any of the synthetic combinations furthercomprise one or more of the following: fungicide, nematicide,bactericide, insecticide, and herbicide.

The invention also features a plurality of any of the syntheticcombinations placed in a medium that promotes plant growth, the mediumselected from the group consisting of: soil, hydroponic apparatus, andartificial growth medium. The invention also features a plurality of anyof the synthetic combinations, wherein the synthetic combinations areshelf-stable.

The invention also features a plant grown from any of the syntheticcombinations disclosed herein, the plant exhibiting an improvedphenotype of agronomic interest, selected from the group consisting of:increased root biomass, increased root length, increased height,increased shoot length, increased leaf number, increased water useefficiency, increased tolerance to low nitrogen stress, increasednitrogen use efficiency, increased overall biomass, increased grainyield, increased photosynthesis rate, increased tolerance to drought,increased heat tolerance, increased salt tolerance, increased resistanceto nematode stress, increased resistance to a fungal pathogen, increasedresistance to a bacterial pathogen, increased resistance to a viralpathogen, a detectable modulation in the level of a metabolite, adetectable modulation in the transcriptome, and a detectable modulationin the proteome.

In some embodiments, the invention features a method for preparing anagricultural seed composition comprising contacting the surface of aplurality of seeds with a formulation comprising a purified microbialpopulation that comprises at least two endophytes that are heterologousto the seed, wherein the first endophyte is capable of metabolizing atleast one of a-D-glucose, arabinose, arbutin, b-methyl-D-galactoside,b-methyl-D-glucoside, D-alanine, D-arabitol, D-aspartic acid,D-cellobiose, dextrin, D-fructose, D-galactose, D-gluconic acid,D-glucosamine, dihydroxyacetone, DL-malic acid, D-mannitol, D-mannose,D-melezitose, D-melibiose, D-raffinose, D-ribose, D-serine, D-threonine,D-trehalose, D-xylose, g-amino-N-butyric acid, g-cyclodextrin, gelatin,gentiobiose, glycogen, glycyl-L-aspartic acid, glycyl-L-glutamic acid,glycyl-L-proline, glyoxylic acid, i-erythritol, inosine, L-alanine,L-alanyl-glycine, L-arabinose, L-asparagine, L-aspartic acid,L-galactonic acid-g-lactone, L-glutamic acid, L-glutamine, L-histidine,L-proline, L-rhamnose, L-serine, L-threonine, maltitol, maltose,maltotriose, mannose, N-acetyl-D-glucosamine, oxalic acid, palatinose,pectin, proline, salicin, stachyose, sucrose, trehalose, turanose,tyramine, uridine, and xylose, wherein the endophytes are present in theformulation in an amount capable of modulating a trait of agronomicimportance, as compared to isoline plants grown from seeds not contactedwith the formulation.

In some embodiments, the invention features a method for preparing anagricultural seed composition, comprising contacting the surface of aplurality of seeds with a formulation comprising a purified microbialpopulation that comprises at least two endophytes that are heterologousto the seed, wherein the first endophyte is capable of at least onefunction or activity selected from the group consisting of auxinproduction, nitrogen fixation, production of an antimicrobial compound,mineral phosphate solubilization, siderophore production, cellulaseproduction, chitinase production, xylanase production, and acetoinproduction, wherein the endophytes are present in the formulation in anamount capable of modulating a trait of agronomic importance, ascompared to isoline plants grown from seeds not contacted with theformulation.

In some embodiments, the invention features a method of improving aphenotype during water limited conditions of a plurality of host plantsgrown from a plurality of seeds, comprising treating the seeds with aformulation comprising at least two endophytes that are heterologous tothe seeds, wherein the first endophyte is capable of metabolizing atleast one of a-D-glucose, arabinose, arbutin, b-methyl-D-galactoside,b-methyl-D-glucoside, D-alanine, D-arabitol, D-aspartic acid,D-cellobiose, dextrin, D-fructose, D-galactose, D-gluconic acid,D-glucosamine, dihydroxyacetone, DL-malic acid, D-mannitol, D-mannose,D-melezitose, D-melibiose, D-raffinose, D-ribose, D-serine, D-threonine,D-trehalose, D-xylose, g-amino-N-butyric acid, g-cyclodextrin, gelatin,gentiobiose, glycogen, glycyl-L-aspartic acid, glycyl-L-glutamic acid,glycyl-L-proline, glyoxylic acid, i-erythritol, inosine, L-alanine,L-alanyl-glycine, L-arabinose, L-asparagine, L-aspartic acid,L-galactonic acid-g-lactone, L-glutamic acid, L-glutamine, L-histidine,L-proline, L-rhamnose, L-serine, L-threonine, maltitol, maltose,maltotriose, mannose, N-acetyl-D-glucosamine, oxalic acid, palatinose,pectin, proline, salicin, stachyose, sucrose, trehalose, turanose,tyramine, uridine, and xylose, the phenotype improvement selected fromthe group consisting of: increased root biomass, increased root length,increased height, increased shoot length, increased leaf number,increased water use efficiency, increased tolerance to low nitrogenstress, increased nitrogen use efficiency, increased overall biomass,increased grain yield, increased photosynthesis rate, increasedtolerance to drought, increased heat tolerance, increased salttolerance, increased resistance to nematode stress, increased resistanceto a fungal pathogen, increased resistance to a bacterial pathogen,increased resistance to a viral pathogen, a detectable modulation in thelevel of a metabolite, a detectable modulation in the transcriptome, anda detectable modulation in the proteome.

In some embodiments of the methods, the first endophyte is a bacterialendophyte. In some embodiments of the methods, the first endophyte is abacterial endophyte and the second endophyte is a bacterial endophyte.In some embodiments of the methods, the first endophyte is a bacterialendophyte and the second endophyte is a fungal endophyte. In someembodiments of the methods, the first endophyte is a fungal endophyte.In some embodiments of the methods, the first endophyte is a fungalendophyte and the second endophyte is a fungal endophyte. In someembodiments of the methods, the first endophyte is a fungal endophyteand the second endophyte is a bacterial endophyte.

In some embodiments of the methods, the first endophyte is capable ofmetabolizing at least two of a-D-glucose, arabinose, arbutin,b-methyl-D-galactoside, b-methyl-D-glucoside, D-alanine, D-arabitol,D-aspartic acid, D-cellobiose, dextrin, D-fructose, D-galactose,D-gluconic acid, D-glucosamine, dihydroxyacetone, DL-malic acid,D-mannitol, D-mannose, D-melezitose, D-melibiose, D-raffinose, D-ribose,D-serine, D-threonine, D-trehalose, D-xylose, g-amino-N-butyric acid,g-cyclodextrin, gelatin, gentiobiose, glycogen, glycyl-L-aspartic acid,glycyl-L-glutamic acid, glycyl-L-proline, glyoxylic acid, i-erythritol,inosine, L-alanine, L-alanyl-glycine, L-arabinose, L-asparagine,L-aspartic acid, L-galactonic acid-g-lactone, L-glutamic acid,L-glutamine, L-histidine, L-proline, L-rhamnose, L-serine, L-threonine,maltitol, maltose, maltotriose, mannose, N-acetyl-D-glucosamine, oxalicacid, palatinose, pectin, proline, salicin, stachyose, sucrose,trehalose, turanose, tyramine, uridine, and xylose.

In some embodiments of the methods, the second endophyte is capable ofmetabolizing at least two of a-D-glucose, arabinose, arbutin,b-methyl-D-galactoside, b-methyl-D-glucoside, D-alanine, D-arabitol,D-aspartic acid, D-cellobiose, dextrin, D-fructose, D-galactose,D-gluconic acid, D-glucosamine, dihydroxyacetone, DL-malic acid,D-mannitol, D-mannose, D-melezitose, D-melibiose, D-raffinose, D-ribose,D-serine, D-threonine, D-trehalose, D-xylose, g-amino-N-butyric acid,g-cyclodextrin, gelatin, gentiobiose, glycogen, glycyl-L-aspartic acid,glycyl-L-glutamic acid, glycyl-L-proline, glyoxylic acid, i-erythritol,inosine, L-alanine, L-alanyl-glycine, L-arabinose, L-asparagine,L-aspartic acid, L-galactonic acid-g-lactone, L-glutamic acid,L-glutamine, L-histidine, L-proline, L-rhamnose, L-serine, L-threonine,maltitol, maltose, maltotriose, mannose, N-acetyl-D-glucosamine, oxalicacid, palatinose, pectin, proline, salicin, stachyose, sucrose,trehalose, turanose, tyramine, uridine, and xylose.

In some embodiments of the methods, the formulation comprises thepurified microbial population at a concentration of at least about 1×102CFU/ml or spores/ml in a liquid formulation or about 1×102 CFU/gm orspores/ml in a non-liquid formulation.

In some embodiments of the methods for preparing an agricultural seedcomposition, the trait of agronomic importance is selected from thegroup consisting of: increased root biomass, increased root length,increased height, increased shoot length, increased leaf number,increased water use efficiency, increased tolerance to low nitrogenstress, increased nitrogen use efficiency, increased overall biomass,increased grain yield, increased photosynthesis rate, increasedtolerance to drought, increased heat tolerance, increased salttolerance, increased resistance to nematode stress, increased resistanceto a fungal pathogen, increased resistance to a bacterial pathogen,increased resistance to a viral pathogen, a detectable modulation in thelevel of a metabolite, a detectable modulation in the transcriptome, anda detectable modulation in the proteome.

In some embodiments of the methods, at least one of the endophytes iscapable of localizing in a plant element of a plant grown from the seed,the plant element selected from the group consisting of: whole plant,seedling, meristematic tissue, ground tissue, vascular tissue, dermaltissue, seed, leaf, root, shoot, stem, flower, fruit, stolon, bulb,tuber, corm, keikis, and bud.

In some embodiments of the methods, at least one of the endophytes iscapable of colonizing a plant element of a plant grown from the seed,the plant element selected from the group consisting of: whole plant,seedling, meristematic tissue, ground tissue, vascular tissue, dermaltissue, seed, leaf, root, shoot, stem, flower, fruit, stolon, bulb,tuber, corm, keikis, and bud.

In some embodiments of the methods, the formulation further comprisesone or more of the following: a stabilizer, or a preservative, or acarrier, or a surfactant, or an anticomplex agent, or any combinationthereof. In some embodiments of the methods, the formulation furthercomprises one or more of the following: fungicide, nematicide,bactericide, insecticide, and herbicide.

In some embodiments of the methods, the seed is a transgenic seed.

The invention also features a plant derived from one of the methods forpreparing an agricultural seed composition, wherein the plant comprisesin at least one of its plant elements the endophytes. In someembodiments, the invention also features progeny of the plant derivedfrom one of the methods for preparing an agricultural seed compositionwherein the progeny comprises in at least one of its plant elements theendophytes.

In some embodiments of any of the methods, the endophyte expresses oneor more genes encoding a protein whose amino acid sequence is at least95%, at least 96%, at least 97%, at least 98%, at least 99%, or 100%identical to an amino acid sequence selected from the group consistingof SEQ ID NOs: 479, 483, 519, 532, 549, 557, 561, 562, 577, 578, 611,626, 640, 656, 660, 666, 674, 676, 677, 678, 679, 680, 682, 683, 684,685, 686, 688, 689, 690, 691, 692, 693, 696, 697, 698, 701, 704, 706,710, 711, 716, 717, 718, 719, 720, 721, 722, 723, 724, 727, 728, 729,730, 731, 732, 733, 734, 735, 737, 738, 741, 743, 744, 745, 746, 747,748, 749, 751, 753, 756, 757, 759, 761, 762, 763, 764, 765, 766, 767,768, 769, 771, 772, 773, 774, 775, 776, 777, 778, 779, 780, 782, 783,784, 785, 786, 788, 790, 793, 795, 796, 797, 798, 800, 801, 802, 803,804, 805, 806, 807, 808, 809, 810, 811, 812, 813, 815, 816, 817, 818,819, 820, 822, 823, 824, 825, 826, 829, 830, 833, 835, 836, 837, 838,839, 840, 841, 842, 843, 844, 846, 848, 850, 851, 853, 854, 855, 856,857, 858, 859, 860, 864, 865, 866, 868, 869, 870, 871, 872, 873, 874,875, 876, 877, 878, 879, 880, 881, 882, 884, 886, 887, 888, 889, 890,891, 892, 893, 894, 895, 897, 898, 899, 901, 902, 903, 904, 905, 906,907, 908, 910, 911, 912, 913, 914, 915, 916, 917, 918, 920, 921, 922,923, 924, 926, 927, 928, 930, 931, 932, 933, 934, 935, 936, 937, 938,939, 940, 941, 942, 943, 944, 945, 946, 947, 948, 949, 950, 952, 953,954, 955, 956, 957, 958, 959, 960, 961, 962, 963, 964, 968, 969, 971,974, 976, 978, 979, 980, 984, 985, 987, 988, 989, 992, 993, 994, 995,996, 998, 1000, 1001, 1002, 1003, 1006, 1008, 1010, 1011, 1012, 1014,1015, 1016, 1017, 1018, 1019, 1021, 1022, 1023, 1024, 1025, 1028, 1029,1030, 1031, 1032, 1033, 1034, 1036, 1037, 1038, 1040, 1041, 1042, 1043,1044, 1045, 1046, 1047, 1048, 1049, 1050, 1051, 1055, 1056, 1058, 1059,1060, 1062, 1064, 1065, 1066, 1068, 1070, 1071, 1072, 1076, 1077, 1079,1080, 1081, 1083, 1085, 1086, 1087, 1088, 1090, 1091, 1092, 1094, 1095,1096, 1097, 1098, 1099, 1101, 1102, 1103, 1104, 1106, 1107, 1108, 1110,1111, 1112, 1113, 1114, 1115, 1116, 1117, 1118, 1119, 1121, 1122, 1123,1124, 1126, 1127, 1129, 1130, 1131, 1132, 1133, 1134, 1136, 1137, 1138,1139, 1140, 1142, 1143, 1144, 1145, 1146, 1147, 1148, 1149, 1151, 1153,1155, 1156, 1157, 1158, 1159, 1160, 1161, 1162, 1163, 1165, 1166, 1167,1168, 1169, 1170, 1171, 1172, 1174, 1176, 1178, 1179, 1180, 1181, 1182,1183, 1184, 1185, 1186, 1188, 1189, 1190, 1191, 1192, 1193, 1194, 1196,1197, 1198, 1199, 1200, 1201, 1203, 1205, 1206, 1207, 1208, 1209, 1210,1211, 1213, 1214, 1216, 1217, 1218, 1219, 1221, 1222, 1223, 1225, 1226,1228, 1229, 1230, 1231, 1232, 1233, 1235, 1237, 1238, 1239, 1241, 1242,1243, 1244, 1245, 1246, 1247, 1248, 1249, 1250, 1251, 1252, 1253, 1255,1256, 1257, 1258, 1259, 1260, 1261, 1262, 1263, 1264, 1265, 1266, 1267,1268, 1269, 1270, 1271, 1272, 1273, 1274, 1275, 1276, 1277, 1279, 1280,1281, 1282, 1283, 1284, 1285, 1286, 1287, 1288, 1290, 1292, 1293, 1296,1297, 1298, 1300, 1301, 1303, 1304, 1306, 1307, 1308, 1309, 1311, 1312,1313, 1314, 1317, 1319, 1320, 1321, 1322, 1323, 1324, 1325, 1326, 1327,1328, 1330, 1331, 1333, 1334, 1335, 1336, 1337, 1338, 1339, 1340, 1341,1342, 1343, 1344, 1345, 1346, 1347, 1348, 1350, 1351, 1352, 1353, 1355,1356, 1357, 1358, 1359, 1360, 1361, 1362, 1363, 1364, 1365, 1366, 1368,1369, 1370, 1371, 1372, 1374, 1375, 1376, 1379, 1380, 1382, 1383, 1384,1385, 1386, 1388, 1389, 1390, 1391, 1392, 1393, 1396, 1397, 1398, 1399,1400, 1402, 1403, 1404, 1405, 1406, 1407, 1408, 1409, 1410, 1411, 1412,1413, 1414, 1415, 1416, 1417, 1418, 1419, 1420, 1421, 1422, 1424, 1425,1426, 1427, 1428, 1430, 1431, 1432, 1433, 1437, 1438, 1439, 1440, 1441,1442, 1443, 1444, 1445, 1446, 1447, 1448, 1449, 1450, 1452, 1453, 1456,1459, 1466, 1467, 1469, 1471, 1478, 1479, 1482, 1483, 1484, 1485, 1487,1488, 1489, 1490, 1495, 1497, 1498, 1499, 1500, 1501, 1504, 1505, 1506,1508, 1511, 1513, 1514, 1516, 1520, 1526, 1529, 1534, 1535, 1537, 1538,1540, 1545, 1547, 1548, 1549, 1550, 1551, 1552, 1553, 1554, 1556, 1559,1561, 1562, 1565, 1566, 1568, 1569, 1570, 1571, 1573, 1574, 1575, 1576,1577, 1578, 1579, 1580, 1581, 1582, 1583, 1585, 1588, 1589, 1591, 1592,1593, 1594, 1595, 1596, 1597, 1598, 1601, 1603, 1604, 1605, 1607, 1608,1609, 1611, 1612, 1613, 1614, 1615, 1616, 1617, 1618, 1619, 1620, 1622,1624, 1625, 1626, 1627, 1628, 1629, 1630, 1632, 1633, 1636, 1637, 1638,1639, 1640, 1641, 1642, 1643, 1644, 1646, 1647, 1648, 1650, 1651, 1652,1654, 1657, 1659, 1660, 1661, 1664, 1665, 1666, 1667, 1668, 1671, 1673,1675, 1676, 1678, 1679, 1681, 1684, 1685, 1686, 1689, 1690, 1692, 1693,1694, 1695, 1696, 1697, 1698, 1701, 1705, 1706, 1707, 1709, 1711, 1712,1713, 1714, 1716, 1717, 1718, 1720, 1721, 1723, 1724, 1725, 1726, 1728,1729, 1731, 1732, 1734, 1735, 1736, 1737, 1738, 1739, 1740, 1741, 1743,1744, 1745, 1746, 1747, 1750, 1751, 1753, 1754, 1755, 1760, 1761, 1762,1763, 1764, 1765, 1767, 1770, 1771, 1772, 1775, 1776, 1777, 1778, 1779,1780, 1781, 1782, 1786, 1787, 1788, 1789, 1791, 1792, 1793, 1794, 1795,1797, 1798, 1799, 1800, 1801, 1803, 1804, 1805, 1806, 1809, 1810, 1811,1814, 1815, 1818, 1819, 1820, 1821, 1822, 1823, 1824, 1825, 1826, 1828,1830, 1831, 1833, 1835, 1836, 1837, 1838, 1839, 1840, 1841, 1842, 1843,1846, 1851, 1852, 1854, 1857, 1858, 1860, 1861, 1862, 1863, 1864, 1866,1868, 1869, 1870, 1872, 1873, 1874, 1875, 1876, 1878, 1879, 1880, 1881,1883, 1884, 1885, 1887, 1888, 1892, 1893, 1894, 1896, 1898, 1899, 1900,1901, 1902, 1903, 1904, 1905, 1906, 1907, 1910, 1911, 1913, 1915, 1916,1917, 1918, 1920, 1921, 1924, 1925, 1926, 1927, 1928, 1930, 1932, 1933,1934, 1935, 1938, 1939, 1940, 1942, 1943, 1945, 1946, 1948, 1949, 1950,1951, 1953, 1954, 1955, 1959, 1960, 1961, 1962, 1963, 1965, 1966, 1967,1970, 1971, 1973, 1975, 1976, 1977, 1979, 1981, 1982, 1983, 1984, 1985,1986, 1988, 1990, 1994, 1995, 1996, 1998, 1999, 2000, 2001, 2002, 2003,2006, 2007, 2008, 2009, 2010, 2011, 2013, 2014, 2015, 2016, 2017, 2018,2019, 2020, 2021, 2022, 2024, 2025, 2026, 2027, 2028, 2029, 2030, 2031,2032, 2034, 2035, 2036, 2037, 2038, 2039, 2040, 2041, 2042, 2043, 2044,2045, 2046, 2047, 2048, 2049, 2050, 2052, 2054, 2055, 2059, 2060, 2062,2065, 2066, 2067, 2068, 2069, 2070, 2071, 2074, 2076, 2077, 2080, 2081,2082, 2083, 2085, 2086, 2087, 2088, 2089, 2090, 2091, 2092, 2093, 2095,2096, 2097, 2098, 2100, 2101, 2102, 2103, 2104, 2105, 2108, 2109, 2110,2112, 2113, 2115, 2116, 2117, 2118, 2119, 2120, 2121, 2125, 2127, 2128,2129, 2131, 2132, 2134, 2135, 2136, 2138, 2140, 2141, 2142, 2143, 2145,2146, 2147, 2148, 2149, 2150, 2153, 2154, 2155, 2156, 2158, 2159, 2160,2162, 2163, 2165, 2166, 2167, 2168, 2169, 2170, 2171, 2172, 2174, 2176,2177, 2179, 2180, 2181, 2182, 2183, 2184, 2185, 2186, 2188, 2190, 2191,2192, 2193, 2194, 2195, 2196, 2197, 2198, 2200, 2202, 2204, 2205, 2206,2207, 2208, 2210, 2211, 2212, 2214, 2215, 2216, 2217, 2218, 2219, 2220,2221, 2222, 2223, 2225, 2226, 2227, 2228, 2229, 2230, 2231, 2232, 2233,2234, 2235, 2236, 2238, 2239, 2241, 2242, 2243, 2244, 2245, 2246, 2248,2249, 2251, 2253, 2254, 2255, 2257, 2258, 2259, 2261, 2262, 2265, 2267,2268, 2269, and 2270.

In some embodiments of the methods, protein expression is modulated inresponse to the first endophyte contacting a plant element. In someembodiments, protein expression is upregulated in response to the firstendophyte contacting a plant element. In some embodiments, the aminoacid sequence of the upregulated protein is at least 95%, at least 96%,at least 97%, at least 98%, at least 99%, or 100% identical to an aminoacid sequence selected from the group consisting of SEQ ID NOs: 549,640, 656, 676, 684, 690, 937, 1456, 1467, 1479, 1484, 1488, 1490, 1498,1499, 1500, 1504, 1505, 1508, 1513, 1529, 1534, 1538, 1540, 1547, 1551,1554, 1561, 1566, 1568, 1570, 1571, 1574, 1578, 1581, 1583, 1591, 1592,1593, 1597, 1598, 1604, 1605, 1609, 1615, 1616, 1619, 1622, 1624, 1626,1629, 1630, 1632, 1636, 1638, 1642, 1643, 1647, 1650, 1651, 1652, 1659,1661, 1664, 1666, 1671, 1675, 1676, 1678, 1684, 1685, 1689, 1692, 1694,1695, 1696, 1701, 1706, 1709, 1711, 1712, 1718, 1723, 1725, 1728, 1729,1732, 1737, 1738, 1740, 1741, 1744, 1746, 1747, 1751, 1755, 1761, 1763,1771, 1772, 1775, 1778, 1779, 1782, 1787, 1788, 1791, 1792, 1797, 1798,1799, 1800, 1805, 1819, 1824, 1828, 1835, 1840, 1842, 1843, 1846, 1854,1860, 1862, 1868, 1875, 1892, 1893, 1900, 1901, 1910, 1918, 1924, 1925,1926, 1928, 1932, 1933, 1934, 1938, 1943, 1946, 1949, 1950, 1953, 1963,1967, 1971, 1973, 1975, 1985, 1990, 1994, 1998, 2000, 2003, 2006, 2010,2013, 2016, 2018, 2021, 2025, 2027, 2028, 2030, 2034, 2035, 2036, 2048,2050, 2052, 2054, 2059, 2062, 2065, 2066, 2067, 2068, 2074, 2080, 2091,2092, 2093, 2095, 2097, 2098, 2100, 2101, 2104, 2108, 2110, 2112, 2117,2119, 2125, 2131, 2134, 2135, 2145, 2149, 2150, 2156, 2159, 2162, 2168,2181, 2185, 2193, 2195, 2196, 2206, 2211, 2216, 2217, 2219, 2220, 2221,2223, 2231, 2236, 2239, 2242, 2243, 2248, 2255, 2257, 2258, 2259, or2262.

In some embodiments of the methods, protein expression is repressed inresponse to the first endophyte contacting a plant element. In someembodiments, the repressed protein amino acid sequence is at least 95%,at least 96%, at least 97%, at least 98%, at least 99%, or 100%identical to a nucleic acid sequence selected from the group consistingof SEQ ID NOs: 479, 483, 519, 532, 557, 626, 674, 678, 680, 683, 685,688, 690, 696, 697, 701, 704, 706, 710, 711, 717, 720, 722, 723, 724,728, 729, 730, 732, 733, 734, 737, 741, 744, 745, 748, 749, 751, 753,756, 757, 761, 764, 766, 768, 769, 772, 773, 774, 778, 779, 782, 783,784, 788, 790, 793, 795, 796, 797, 800, 802, 803, 806, 807, 808, 810,812, 817, 818, 819, 820, 822, 825, 826, 833, 836, 837, 839, 841, 846,848, 851, 853, 854, 855, 856, 857, 860, 864, 865, 866, 870, 872, 874,876, 878, 879, 880, 881, 882, 884, 886, 887, 890, 891, 893, 894, 895,898, 901, 903, 905, 907, 908, 910, 911, 912, 913, 915, 917, 918, 921,924, 926, 927, 928, 933, 934, 935, 936, 937, 938, 940, 942, 944, 945,946, 947, 950, 952, 954, 955, 957, 960, 961, 962, 963, 964, 968, 971,976, 978, 979, 985, 987, 989, 992, 1000, 1001, 1002, 1003, 1006, 1008,1012, 1014, 1018, 1019, 1021, 1022, 1024, 1025, 1028, 1031, 1032, 1034,1037, 1038, 1040, 1042, 1043, 1046, 1047, 1050, 1051, 1056, 1059, 1064,1065, 1068, 1070, 1072, 1077, 1079, 1083, 1086, 1087, 1091, 1094, 1095,1098, 1102, 1103, 1104, 1110, 1111, 1112, 1113, 1114, 1116, 1117, 1118,1121, 1126, 1130, 1132, 1133, 1134, 1136, 1139, 1143, 1146, 1147, 1151,1155, 1156, 1158, 1159, 1160, 1162, 1163, 1165, 1168, 1170, 1172, 1174,1176, 1180, 1182, 1183, 1186, 1188, 1192, 1193, 1194, 1196, 1197, 1198,1209, 1214, 1217, 1218, 1219, 1221, 1222, 1223, 1225, 1226, 1230, 1237,1242, 1244, 1249, 1251, 1253, 1256, 1260, 1261, 1262, 1264, 1270, 1272,1274, 1276, 1279, 1280, 1283, 1284, 1285, 1286, 1288, 1290, 1292, 1298,1300, 1303, 1307, 1309, 1311, 1312, 1313, 1320, 1321, 1324, 1325, 1328,1330, 1331, 1333, 1336, 1337, 1339, 1340, 1344, 1346, 1352, 1353, 1355,1357, 1358, 1359, 1360, 1361, 1363, 1364, 1365, 1370, 1375, 1376, 1379,1380, 1383, 1384, 1386, 1390, 1391, 1392, 1393, 1396, 1399, 1400, 1402,1405, 1408, 1411, 1412, 1418, 1420, 1422, 1427, 1428, 1431, 1433, 1438,1439, 1440, 1442, 1444, 1445, 1449, or 1450.

In some embodiments of the methods, the protein is expressed with atleast a two-fold difference, at least a three-fold difference, at leasta four-fold difference, at least a five-fold difference, at least asix-fold difference, at least a seven-fold difference, at least aneight-fold difference, at least a nine-fold difference, at least aten-fold difference or more in expression level as compared to theprotein expression level of a reference microorganism. In someembodiments, the difference in expression level of the protein ispositive. In some embodiments, the difference in expression level of theprotein is negative.

In some embodiments of the methods, the protein is involved in at leastone KEGG pathway selected from the group consisting of: endocytosis,purine metabolism, inositol phosphate metabolism, and peroxisome. Insome embodiments of the methods, the protein is involved in at least oneKEGG pathway selected from the group consisting of: ko00403 (indolediterpene alkaloid biosynthesis), ko00522 (biosynthesis of 12-, 14- and16-membered macrolides), ko00550 (peptidoglycan biosynthesis), ko00601(glycosphingolipid biosynthesis-lacto and neolacto series), ko0901(indole alkaloid biosynthesis), ko01052 (type I polyketide structures),ko010503 (biosynthesis of siderophore group nonribosomal peptides),ko01501 (beta-Lactam resistance), and ko04071 (sphingolipid signalingpathway).

In some embodiments of any of the methods, the plant, crop, seedling, orplant grown from the seed expresses one or more genes whose nucleic acidsequence is at least 95%, at least 96%, at least 97%, at least 98%, atleast 99%, or 100% identical to a nucleic acid sequence selected fromthe group consisting of SEQ ID NOs: 4127, 4128, 4129, 4130, 4131, 4132,4133, 4134, 4135, 4136, 4137, 4138, 4139, 4140, 4141, 4142, 4143, 4144,4145, 4146, 4147, 4148, 4149, 4150, 4151, 4152, 4153, 4154, 4155, 4156,4157, 4158, 4159, 4160, 4161, 4162, 4163, 4164, 4165, 4166, 4167, 4168,4169, 4170, 4171, 4172, 4173, 4174, 4175, 4176, 4177, 4178, 4179, 4180,4181, 4182, 4183, 4184, 4185, 4186, 4187, 4188, 4189, 4190, 4191, 4192,4193, 4194, 4195, 4196, 4197, 4198, 4199, 4200, 4201, 4202, 4203, 4204,4205, 4206, 4207, 4208, 4209, 4210, 4211, 4212, 4213, 4214, 4215, 4216,4217, 4218, 4219, 4220, 4221, 4222, 4223, 4224, 4225, 4226, 4227, 4228,4229, 4230, 4231, 4232, 4233, 4234, 4235, 4236, 4237, 4238, 4239, 4240,4241, 4242, 4243, 4244, 4245, 4246, 4247, 4248, 4249, 4250, 4251, 4252,4253, 4254, 4255, 4256, 4257, 4258, 4259, 4260, 4261, 4262, 4263, 4264,4265, 4266, 4267, 4268, or 4269.

In some embodiments, the one or more plant genes are modulated inresponse to the first endophyte contacting the plant or plant element ascompared to a reference microorganism contacting the plant or plantelement. In some embodiments, the one or more plant genes areupregulated in response to the first endophyte contacting a plantelement as compared to a reference microorganism contacting the plant orplant element. In some embodiments, the upregulated genes nucleic acidsequence is at least 95%, at least 96%, at least 97%, at least 98%, atleast 99%, or 100% identical to a nucleic acid sequence selected fromthe group consisting of SEQ ID NOs: 4131, 4140, 4142, 4153, 4162, 4167,4181, 4183, 4184, 4195, 4199, 4201, 4206, 4213, 4222, 4223, 4250, 4253,or 4269.

In some embodiments, the transcription of one or more genes arerepressed in response to the first endophyte contacting a plant elementas compared to a reference microorganism contacting the plant or plantelement. In some embodiments, the repressed genes nucleic acid sequenceis at least 95%, at least 96%, at least 97%, at least 98%, at least 99%,or 100% identical to a nucleic acid sequence selected from the groupconsisting of SEQ ID NOs: 4150.

In some embodiments, the one or more genes are expressed with at least a0.5-fold difference, at least a 0.6-fold difference, at least a 0.7-folddifference, at least a 0.8-fold difference, at least a 0.9-folddifference, at least a 1.0-fold difference, at least a 1.1-folddifference, at least a 1.2-fold difference, at least a 1.3-folddifference or more in expression level as compared to the geneexpression level of a reference microorganism. In some embodiments, thedifference in expression level is positive. In some embodiments, thedifference in expression level is negative.

In some embodiments, the one or more genes has at least one genefunction selected from the group consisting of: cell wall modification,defense response, oxidation-reduction process, biological process,regulation of transcription, metabolic process, glucosinolatebiosynthetic process, response to karrikin, protein phosphorylation,protein folding, response to chitin, proteolysis, response to auxinstimulus, DNA-dependent regulation of transcription, N-terminal proteinmyristoylation, response to oxidative stress, cellular component, leafsenescence, resistance gene-dependent defense response signalingpathway, zinc ion binding, response to cold, malate metabolic process,transport, catalytic activity, response to ozone, VQ motif, regulationof systemic acquired resistance, potassium ion transport, anaerobicrespiration, multicellular organismal development, response to heat,methyltransferase activity, response to wounding, oxidation-reductionprocess, monooxygenase activity, oxidation-reduction process,carbohydrate metabolic process, exocytosis, nuclear-transcribed mRNApoly(A) tail shortening, sodium ion transport, glycerol metabolicprocess, on willebrand factor A3, response to water deprivation,response to salt stress, and chlorophyll biosynthetic process. In someembodiments, the gene has a gene ontology (GO) identifier selected fromthe group consisting of: GO:0003824, GO, catalytic activity; GO:0006355,GO, regulation of transcription, DNA-dependent; GO:0009870, GO, defenseresponse signaling pathway, resistance gene-dependent; GO:0008150, GO,biological process; GO:0010200, GO, response to chitin; GO:0006508, GO,proteolysis; GO:0010193, GO, response to ozone; GO:0006979, GO, responseto oxidative stress; and GO:0005975, GO, carbohydrate metabolic process.

In some embodiments, the gene function is selected from the followinggroup: single-stranded DNA specific endodeoxyribonuclease activity,sequence-specific DNA binding transcription factor activity,NAD+ADP-ribosyltransferase activity, metalloendopeptidase activity, DNAcatabolic process, cellular iron ion homeostasis, response to osmoticstress, metallopeptidase activity, zinc ion binding, response towounding, camalexin biosynthetic process, endoribonuclease activity,producing 5′-phosphomonoesters, cellular response to heat, T/Gmismatch-specific endonuclease activity, polyamine oxidase activity,flavin adenine dinucleotide binding, cellular heat acclimation, cellularresponse to ethylene stimulus, cellular response to nitric oxide, andreactive oxygen species metabolic process.

In some embodiments, the endophyte comprises an ITS rRNA nucleic acidsequence at least 95%, at least 96%, at least 97%, at least 98%, atleast 99%, or 100% identical to the nucleic acid sequence of SEQ ID NO:344.

In some embodiments of any of the methods, the endophyte expresses oneor more genes encoding a protein whose amino acid sequence is at least95%, at least 96%, at least 97%, at least 98%, at least 99%, or 100%identical to an amino acid sequence selected from the group consistingof SEQ ID NOs: 477-501, 505, 514, 518, 521, 528, 530, 531, 550, 566,567, 572, 579, 580, 581, 587, 593, 600, 602, 614, 623, 630, 635, 643,645, 652, 657, 661, 662, 667, 670, 672, 673, 4510-4535, 4540, 4541,4542, 4547, 4555, 4558, 4560, 4569, 4570, 4571, 4572, 4577, 4582, 4592,4594, 4602, 4608, 4609, 4622, 4626, 4641, 4643, 4653, 4654, 4742-4766,4734, 4739, 4740, 477, 478, 480, 482, 484, 485, 487, 489, 494, 496, 497,501, 530, 567, 587, 602, 614, 633, 645, 649, 651, 652, 658, 665, 666,667, 673, 874, 934, 1013, 1249, 1342, 2252, 2272, 2273, 2281, 2282,2284, 2285, 2286, 2287, 2289, 2290, 2291, 2292, 2293, 2296, 4510, 4514,4515, 4518, 4520, 4521, 4525, 4526, 4527, 4529, 4532, 4538, 4539, 4540,4555, 4559, 4560, 4562, 4569, 4570, 4571, 4572, 4577, 4581, 4582, 4594,4595, 4597, 4608, 4615, 4618, 4623, 4624, 4626, 4630, 4632, 4635, 4641,4642, 4646, 4650, 4658, 4659, 4661, 4662, 4663, 4666, 4667, 4668, 4670,4799, 4801, 4802, 4803, 4804, 4805, 4826, 4827, 4828, 4829, 4830, 4831,4832, 4833, 4834, 4835, 4836, 4837, 4838, 4839, 4840, 4841, 4863, 4864,4865, 4866, 4867, 4868, 4869, 4870, 4871, 4872, 4873, 4874, 4875, 4876,4877, 4878, 4879, 4880, 4881, 4882, 4883, 4884, 4885, 4886, 4887, 4888,4889, 4890, 4891, 4892, 4893, 4894, 4917, 4918, 4919, 4920, 4921, 4922,4923, 4924, 4925, 4939, 4940, 4941, 4943, 4947, 4948, 4950, 4951, 4955,4956, 4957, 2315, 2320, 2322, 2326, 2349, 2350, 2352, 2377, 2382, 2390,2407, 2422, 2436, 2443, 2457, 2463, 2464, 2470, 2477, 2483, 2721, 2968,3093, 3185, 4096, 4097, 4098, 4099, 4100, 4101, 4102, 4103, 4104, 4105,4106, 4107, 4108, 4109, 4110, 4111, 4112, 4113, 4114, 4115, 4116, 4117,4118, 4119, 4120, 4121, 4122, 4123, 4124, 4125, 4126, 4346, 4353, 4362,4369, 4386, 4391, 4394, 4408, 4410, 4413, 4415, 4422, 4423, 4432, 4433,4442, 4469, 4487, 4489, 4491, 4493, 4494, 4495, 4496, 4497, 4498, 4499,4500, 4501, 4502, 4503, 4504, 4505, 4506, 4507, 4508, 4509, 4343, 4484,4485, 4486, 4488, 4490, and 4492. In some embodiments of any of themethods, the endophyte expresses one or more genes involved in starchand sucrose metabolism, cell wall degradation, or protection fromoxidative stress.

In some embodiments, the protein is expressed with at least a two-folddifference, at least a three-fold difference, at least a four-folddifference, at least a five-fold difference, at least a six-folddifference, at least a seven-fold difference, at least an eight-folddifference, at least a nine-fold difference, at least a ten-folddifference or more in expression level as compared to the proteinexpression level of a reference microorganism. In some embodiments, thedifference in expression level is positive. In some embodiments, thedifference in expression level is negative.

In some embodiments, the endophyte comprises an ITS rRNA nucleic acidsequence at least 95%, at least 96%, at least 97%, at least 98%, atleast 99%, or 100% identical to a nucleic acid sequence selected fromthe group consisting of SEQ ID NOs: 344 and 447. In some embodiments,the endophyte comprises a 16S rRNA nucleic acid sequence at least 95%,at least 96%, at least 97%, at least 98%, at least 99%, or 100%identical to a nucleic acid sequence selected from the group consistingof SEQ ID NOs: 439 or 441.

In some embodiments of any of the methods, the endophyte expresses oneor more genes encoding a protein whose amino acid sequence is at least95%, at least 96%, at least 97%, at least 98%, at least 99%, or 100%identical to an amino acid sequence selected from the group consistingof SEQ ID NOs: 479, 483, 519, 532, 549, 557, 561, 562, 577, 578, 611,626, 640, 656, 660, 666, 674, 676, 677, 678, 679, 680, 682, 683, 684,685, 686, 688, 689, 690, 691, 692, 693, 696, 697, 698, 701, 704, 706,710, 711, 716, 717, 718, 719, 720, 721, 722, 723, 724, 727, 728, 729,730, 731, 732, 733, 734, 735, 737, 738, 741, 743, 744, 745, 746, 747,748, 749, 751, 753, 756, 757, 759, 761, 762, 763, 764, 765, 766, 767,768, 769, 771, 772, 773, 774, 775, 776, 777, 778, 779, 780, 782, 783,784, 785, 786, 788, 790, 793, 795, 796, 797, 798, 800, 801, 802, 803,804, 805, 806, 807, 808, 809, 810, 811, 812, 813, 815, 816, 817, 818,819, 820, 822, 823, 824, 825, 826, 829, 830, 833, 835, 836, 837, 838,839, 840, 841, 842, 843, 844, 846, 848, 850, 851, 853, 854, 855, 856,857, 858, 859, 860, 864, 865, 866, 868, 869, 870, 871, 872, 873, 874,875, 876, 877, 878, 879, 880, 881, 882, 884, 886, 887, 888, 889, 890,891, 892, 893, 894, 895, 897, 898, 899, 901, 902, 903, 904, 905, 906,907, 908, 910, 911, 912, 913, 914, 915, 916, 917, 918, 920, 921, 922,923, 924, 926, 927, 928, 930, 931, 932, 933, 934, 935, 936, 937, 938,939, 940, 941, 942, 943, 944, 945, 946, 947, 948, 949, 950, 952, 953,954, 955, 956, 957, 958, 959, 960, 961, 962, 963, 964, 968, 969, 971,974, 976, 978, 979, 980, 984, 985, 987, 988, 989, 992, 993, 994, 995,996, 998, 1000, 1001, 1002, 1003, 1006, 1008, 1010, 1011, 1012, 1014,1015, 1016, 1017, 1018, 1019, 1021, 1022, 1023, 1024, 1025, 1028, 1029,1030, 1031, 1032, 1033, 1034, 1036, 1037, 1038, 1040, 1041, 1042, 1043,1044, 1045, 1046, 1047, 1048, 1049, 1050, 1051, 1055, 1056, 1058, 1059,1060, 1062, 1064, 1065, 1066, 1068, 1070, 1071, 1072, 1076, 1077, 1079,1080, 1081, 1083, 1085, 1086, 1087, 1088, 1090, 1091, 1092, 1094, 1095,1096, 1097, 1098, 1099, 1101, 1102, 1103, 1104, 1106, 1107, 1108, 1110,1111, 1112, 1113, 1114, 1115, 1116, 1117, 1118, 1119, 1121, 1122, 1123,1124, 1126, 1127, 1129, 1130, 1131, 1132, 1133, 1134, 1136, 1137, 1138,1139, 1140, 1142, 1143, 1144, 1145, 1146, 1147, 1148, 1149, 1151, 1153,1155, 1156, 1157, 1158, 1159, 1160, 1161, 1162, 1163, 1165, 1166, 1167,1168, 1169, 1170, 1171, 1172, 1174, 1176, 1178, 1179, 1180, 1181, 1182,1183, 1184, 1185, 1186, 1188, 1189, 1190, 1191, 1192, 1193, 1194, 1196,1197, 1198, 1199, 1200, 1201, 1203, 1205, 1206, 1207, 1208, 1209, 1210,1211, 1213, 1214, 1216, 1217, 1218, 1219, 1221, 1222, 1223, 1225, 1226,1228, 1229, 1230, 1231, 1232, 1233, 1235, 1237, 1238, 1239, 1241, 1242,1243, 1244, 1245, 1246, 1247, 1248, 1249, 1250, 1251, 1252, 1253, 1255,1256, 1257, 1258, 1259, 1260, 1261, 1262, 1263, 1264, 1265, 1266, 1267,1268, 1269, 1270, 1271, 1272, 1273, 1274, 1275, 1276, 1277, 1279, 1280,1281, 1282, 1283, 1284, 1285, 1286, 1287, 1288, 1290, 1292, 1293, 1296,1297, 1298, 1300, 1301, 1303, 1304, 1306, 1307, 1308, 1309, 1311, 1312,1313, 1314, 1317, 1319, 1320, 1321, 1322, 1323, 1324, 1325, 1326, 1327,1328, 1330, 1331, 1333, 1334, 1335, 1336, 1337, 1338, 1339, 1340, 1341,1342, 1343, 1344, 1345, 1346, 1347, 1348, 1350, 1351, 1352, 1353, 1355,1356, 1357, 1358, 1359, 1360, 1361, 1362, 1363, 1364, 1365, 1366, 1368,1369, 1370, 1371, 1372, 1374, 1375, 1376, 1379, 1380, 1382, 1383, 1384,1385, 1386, 1388, 1389, 1390, 1391, 1392, 1393, 1396, 1397, 1398, 1399,1400, 1402, 1403, 1404, 1405, 1406, 1407, 1408, 1409, 1410, 1411, 1412,1413, 1414, 1415, 1416, 1417, 1418, 1419, 1420, 1421, 1422, 1424, 1425,1426, 1427, 1428, 1430, 1431, 1432, 1433, 1437, 1438, 1439, 1440, 1441,1442, 1443, 1444, 1445, 1446, 1447, 1448, 1449, 1450, 1452, 1453, 1456,1459, 1466, 1467, 1469, 1471, 1478, 1479, 1482, 1483, 1484, 1485, 1487,1488, 1489, 1490, 1495, 1497, 1498, 1499, 1500, 1501, 1504, 1505, 1506,1508, 1511, 1513, 1514, 1516, 1520, 1526, 1529, 1534, 1535, 1537, 1538,1540, 1545, 1547, 1548, 1549, 1550, 1551, 1552, 1553, 1554, 1556, 1559,1561, 1562, 1565, 1566, 1568, 1569, 1570, 1571, 1573, 1574, 1575, 1576,1577, 1578, 1579, 1580, 1581, 1582, 1583, 1585, 1588, 1589, 1591, 1592,1593, 1594, 1595, 1596, 1597, 1598, 1601, 1603, 1604, 1605, 1607, 1608,1609, 1611, 1612, 1613, 1614, 1615, 1616, 1617, 1618, 1619, 1620, 1622,1624, 1625, 1626, 1627, 1628, 1629, 1630, 1632, 1633, 1636, 1637, 1638,1639, 1640, 1641, 1642, 1643, 1644, 1646, 1647, 1648, 1650, 1651, 1652,1654, 1657, 1659, 1660, 1661, 1664, 1665, 1666, 1667, 1668, 1671, 1673,1675, 1676, 1678, 1679, 1681, 1684, 1685, 1686, 1689, 1690, 1692, 1693,1694, 1695, 1696, 1697, 1698, 1701, 1705, 1706, 1707, 1709, 1711, 1712,1713, 1714, 1716, 1717, 1718, 1720, 1721, 1723, 1724, 1725, 1726, 1728,1729, 1731, 1732, 1734, 1735, 1736, 1737, 1738, 1739, 1740, 1741, 1743,1744, 1745, 1746, 1747, 1750, 1751, 1753, 1754, 1755, 1760, 1761, 1762,1763, 1764, 1765, 1767, 1770, 1771, 1772, 1775, 1776, 1777, 1778, 1779,1780, 1781, 1782, 1786, 1787, 1788, 1789, 1791, 1792, 1793, 1794, 1795,1797, 1798, 1799, 1800, 1801, 1803, 1804, 1805, 1806, 1809, 1810, 1811,1814, 1815, 1818, 1819, 1820, 1821, 1822, 1823, 1824, 1825, 1826, 1828,1830, 1831, 1833, 1835, 1836, 1837, 1838, 1839, 1840, 1841, 1842, 1843,1846, 1851, 1852, 1854, 1857, 1858, 1860, 1861, 1862, 1863, 1864, 1866,1868, 1869, 1870, 1872, 1873, 1874, 1875, 1876, 1878, 1879, 1880, 1881,1883, 1884, 1885, 1887, 1888, 1892, 1893, 1894, 1896, 1898, 1899, 1900,1901, 1902, 1903, 1904, 1905, 1906, 1907, 1910, 1911, 1913, 1915, 1916,1917, 1918, 1920, 1921, 1924, 1925, 1926, 1927, 1928, 1930, 1932, 1933,1934, 1935, 1938, 1939, 1940, 1942, 1943, 1945, 1946, 1948, 1949, 1950,1951, 1953, 1954, 1955, 1959, 1960, 1961, 1962, 1963, 1965, 1966, 1967,1970, 1971, 1973, 1975, 1976, 1977, 1979, 1981, 1982, 1983, 1984, 1985,1986, 1988, 1990, 1994, 1995, 1996, 1998, 1999, 2000, 2001, 2002, 2003,2006, 2007, 2008, 2009, 2010, 2011, 2013, 2014, 2015, 2016, 2017, 2018,2019, 2020, 2021, 2022, 2024, 2025, 2026, 2027, 2028, 2029, 2030, 2031,2032, 2034, 2035, 2036, 2037, 2038, 2039, 2040, 2041, 2042, 2043, 2044,2045, 2046, 2047, 2048, 2049, 2050, 2052, 2054, 2055, 2059, 2060, 2062,2065, 2066, 2067, 2068, 2069, 2070, 2071, 2074, 2076, 2077, 2080, 2081,2082, 2083, 2085, 2086, 2087, 2088, 2089, 2090, 2091, 2092, 2093, 2095,2096, 2097, 2098, 2100, 2101, 2102, 2103, 2104, 2105, 2108, 2109, 2110,2112, 2113, 2115, 2116, 2117, 2118, 2119, 2120, 2121, 2125, 2127, 2128,2129, 2131, 2132, 2134, 2135, 2136, 2138, 2140, 2141, 2142, 2143, 2145,2146, 2147, 2148, 2149, 2150, 2153, 2154, 2155, 2156, 2158, 2159, 2160,2162, 2163, 2165, 2166, 2167, 2168, 2169, 2170, 2171, 2172, 2174, 2176,2177, 2179, 2180, 2181, 2182, 2183, 2184, 2185, 2186, 2188, 2190, 2191,2192, 2193, 2194, 2195, 2196, 2197, 2198, 2200, 2202, 2204, 2205, 2206,2207, 2208, 2210, 2211, 2212, 2214, 2215, 2216, 2217, 2218, 2219, 2220,2221, 2222, 2223, 2225, 2226, 2227, 2228, 2229, 2230, 2231, 2232, 2233,2234, 2235, 2236, 2238, 2239, 2241, 2242, 2243, 2244, 2245, 2246, 2248,2249, 2251, 2253, 2254, 2255, 2257, 2258, 2259, 2261, 2262, 2265, 2267,2268, 2269, and 2270.

In some embodiments of any of the methods, expression of the protein ismodulated in response to the first endophyte contacting a plant element.

In some embodiments, expression of the protein is upregulated inresponse to the first endophyte contacting a plant element. In someembodiments, the amino acid sequence of the upregulated protein is atleast 95%, at least 96%, at least 97%, at least 98%, at least 99%, or100% identical to an amino acid sequence selected from the groupconsisting of SEQ ID NOs: 549, 640, 656, 676, 684, 690, 937, 1456, 1467,1479, 1484, 1488, 1490, 1498, 1499, 1500, 1504, 1505, 1508, 1513, 1529,1534, 1538, 1540, 1547, 1551, 1554, 1561, 1566, 1568, 1570, 1571, 1574,1578, 1581, 1583, 1591, 1592, 1593, 1597, 1598, 1604, 1605, 1609, 1615,1616, 1619, 1622, 1624, 1626, 1629, 1630, 1632, 1636, 1638, 1642, 1643,1647, 1650, 1651, 1652, 1659, 1661, 1664, 1666, 1671, 1675, 1676, 1678,1684, 1685, 1689, 1692, 1694, 1695, 1696, 1701, 1706, 1709, 1711, 1712,1718, 1723, 1725, 1728, 1729, 1732, 1737, 1738, 1740, 1741, 1744, 1746,1747, 1751, 1755, 1761, 1763, 1771, 1772, 1775, 1778, 1779, 1782, 1787,1788, 1791, 1792, 1797, 1798, 1799, 1800, 1805, 1819, 1824, 1828, 1835,1840, 1842, 1843, 1846, 1854, 1860, 1862, 1868, 1875, 1892, 1893, 1900,1901, 1910, 1918, 1924, 1925, 1926, 1928, 1932, 1933, 1934, 1938, 1943,1946, 1949, 1950, 1953, 1963, 1967, 1971, 1973, 1975, 1985, 1990, 1994,1998, 2000, 2003, 2006, 2010, 2013, 2016, 2018, 2021, 2025, 2027, 2028,2030, 2034, 2035, 2036, 2048, 2050, 2052, 2054, 2059, 2062, 2065, 2066,2067, 2068, 2074, 2080, 2091, 2092, 2093, 2095, 2097, 2098, 2100, 2101,2104, 2108, 2110, 2112, 2117, 2119, 2125, 2131, 2134, 2135, 2145, 2149,2150, 2156, 2159, 2162, 2168, 2181, 2185, 2193, 2195, 2196, 2206, 2211,2216, 2217, 2219, 2220, 2221, 2223, 2231, 2236, 2239, 2242, 2243, 2248,2255, 2257, 2258, 2259, or 2262.

In some embodiments, expression of the protein is repressed in responseto the first endophyte contacting a plant element. In some embodiments,the repressed protein amino acid sequence is at least 95%, at least 96%,at least 97%, at least 98%, at least 99%, or 100% identical to a nucleicacid sequence selected from the group consisting of SEQ ID NOs: 479,483, 519, 532, 557, 626, 674, 678, 680, 683, 685, 688, 690, 696, 697,701, 704, 706, 710, 711, 717, 720, 722, 723, 724, 728, 729, 730, 732,733, 734, 737, 741, 744, 745, 748, 749, 751, 753, 756, 757, 761, 764,766, 768, 769, 772, 773, 774, 778, 779, 782, 783, 784, 788, 790, 793,795, 796, 797, 800, 802, 803, 806, 807, 808, 810, 812, 817, 818, 819,820, 822, 825, 826, 833, 836, 837, 839, 841, 846, 848, 851, 853, 854,855, 856, 857, 860, 864, 865, 866, 870, 872, 874, 876, 878, 879, 880,881, 882, 884, 886, 887, 890, 891, 893, 894, 895, 898, 901, 903, 905,907, 908, 910, 911, 912, 913, 915, 917, 918, 921, 924, 926, 927, 928,933, 934, 935, 936, 937, 938, 940, 942, 944, 945, 946, 947, 950, 952,954, 955, 957, 960, 961, 962, 963, 964, 968, 971, 976, 978, 979, 985,987, 989, 992, 1000, 1001, 1002, 1003, 1006, 1008, 1012, 1014, 1018,1019, 1021, 1022, 1024, 1025, 1028, 1031, 1032, 1034, 1037, 1038, 1040,1042, 1043, 1046, 1047, 1050, 1051, 1056, 1059, 1064, 1065, 1068, 1070,1072, 1077, 1079, 1083, 1086, 1087, 1091, 1094, 1095, 1098, 1102, 1103,1104, 1110, 1111, 1112, 1113, 1114, 1116, 1117, 1118, 1121, 1126, 1130,1132, 1133, 1134, 1136, 1139, 1143, 1146, 1147, 1151, 1155, 1156, 1158,1159, 1160, 1162, 1163, 1165, 1168, 1170, 1172, 1174, 1176, 1180, 1182,1183, 1186, 1188, 1192, 1193, 1194, 1196, 1197, 1198, 1209, 1214, 1217,1218, 1219, 1221, 1222, 1223, 1225, 1226, 1230, 1237, 1242, 1244, 1249,1251, 1253, 1256, 1260, 1261, 1262, 1264, 1270, 1272, 1274, 1276, 1279,1280, 1283, 1284, 1285, 1286, 1288, 1290, 1292, 1298, 1300, 1303, 1307,1309, 1311, 1312, 1313, 1320, 1321, 1324, 1325, 1328, 1330, 1331, 1333,1336, 1337, 1339, 1340, 1344, 1346, 1352, 1353, 1355, 1357, 1358, 1359,1360, 1361, 1363, 1364, 1365, 1370, 1375, 1376, 1379, 1380, 1383, 1384,1386, 1390, 1391, 1392, 1393, 1396, 1399, 1400, 1402, 1405, 1408, 1411,1412, 1418, 1420, 1422, 1427, 1428, 1431, 1433, 1438, 1439, 1440, 1442,1444, 1445, 1449, or 1450.

In some embodiments, the protein is expressed with at least a two-folddifference, at least a three-fold difference, at least a four-folddifference, at least a five-fold difference, at least a six-folddifference, at least a seven-fold difference, at least an eight-folddifference, at least a nine-fold difference, at least a ten-folddifference or more in expression level as compared to the proteinexpression level of a reference microorganism. In some embodiments ofany of the methods, the difference in expression level is positive. Insome embodiments, the difference in expression level is negative.

In some embodiments, the protein is involved in at least one KEGGpathway selected from the group consisting of: endocytosis, purinemetabolism, inositol phosphate metabolism, and peroxisome. In someembodiments, the protein is involved in at least one KEGG pathwayselected from the group consisting of: ko00403 (indole diterpenealkaloid biosynthesis), ko00522 (biosynthesis of 12-, 14- and16-membered macrolides), ko00550 (peptidoglycan biosynthesis), ko00601(glycosphingolipid biosynthesis—lacto and neolacto series), ko0901(indole alkaloid biosynthesis), ko01052 (type I polyketide structures),ko010503 (biosynthesis of siderophore group nonribosomal peptides),ko01501 (beta-Lactam resistance), and ko04071 (sphingolipid signalingpathway).

In some embodiments of any of the plants, formulations, syntheticcombinations, or other compositions of the invention, the plant, crop,seedling, or plant grown from the seed expresses one or more genes whosenucleic acid sequence is at least 95%, at least 96%, at least 97%, atleast 98%, at least 99%, or 100% identical to a nucleic acid sequenceselected from the group consisting of SEQ ID NOs: 4127, 4128, 4129,4130, 4131, 4132, 4133, 4134, 4135, 4136, 4137, 4138, 4139, 4140, 4141,4142, 4143, 4144, 4145, 4146, 4147, 4148, 4149, 4150, 4151, 4152, 4153,4154, 4155, 4156, 4157, 4158, 4159, 4160, 4161, 4162, 4163, 4164, 4165,4166, 4167, 4168, 4169, 4170, 4171, 4172, 4173, 4174, 4175, 4176, 4177,4178, 4179, 4180, 4181, 4182, 4183, 4184, 4185, 4186, 4187, 4188, 4189,4190, 4191, 4192, 4193, 4194, 4195, 4196, 4197, 4198, 4199, 4200, 4201,4202, 4203, 4204, 4205, 4206, 4207, 4208, 4209, 4210, 4211, 4212, 4213,4214, 4215, 4216, 4217, 4218, 4219, 4220, 4221, 4222, 4223, 4224, 4225,4226, 4227, 4228, 4229, 4230, 4231, 4232, 4233, 4234, 4235, 4236, 4237,4238, 4239, 4240, 4241, 4242, 4243, 4244, 4245, 4246, 4247, 4248, 4249,4250, 4251, 4252, 4253, 4254, 4255, 4256, 4257, 4258, 4259, 4260, 4261,4262, 4263, 4264, 4265, 4266, 4267, 4268, or 4269.

In some embodiments, the one or more plant genes are modulated inresponse to the first endophyte contacting the plant or plant element ascompared to a reference microorganism contacting the plant or plantelement.

In some embodiments, the one or more plant genes are upregulated inresponse to the first endophyte contacting a plant element as comparedto a reference microorganism contacting the plant or plant element. Insome embodiments, the upregulated gene's nucleic acid sequence is atleast 95%, at least 96%, at least 97%, at least 98%, at least 99%, or100% identical to a nucleic acid sequence selected from the groupconsisting of SEQ ID NOs: 4131, 4140, 4142, 4153, 4162, 4167, 4181,4183, 4184, 4195, 4199, 4201, 4206, 4213, 4222, 4223, 4250, 4253, or4269.

In some embodiments, the transcription of one or more genes arerepressed in response to the first endophyte contacting a plant elementas compared to a reference microorganism contacting the plant or plantelement. In some embodiments, the repressed genes nucleic acid sequenceis at least 95%, at least 96%, at least 97%, at least 98%, at least 99%,or 100% identical to a nucleic acid sequence selected from the groupconsisting of SEQ ID NOs: 4150.

In some embodiments, the one or more genes are expressed with at least a0.5-fold difference, at least a 0.6-fold difference, at least a 0.7-folddifference, at least a 0.8-fold difference, at least a 0.9-folddifference, at least a 1.0-fold difference, at least a 1.1-folddifference, at least a 1.2-fold difference, at least a 1.3-folddifference or more in expression level as compared to the geneexpression level of a reference microorganism. In some embodiments, thedifference in expression level is positive. In some embodiments, thedifference in expression level is negative.

In some embodiments, the one or more genes has at least one genefunction selected from the group consisting of: cell wall modification,defense response, oxidation-reduction process, biological process,regulation of transcription, metabolic process, glucosinolatebiosynthetic process, response to karrikin, protein phosphorylation,protein folding, response to chitin, proteolysis, response to auxinstimulus, DNA-dependent regulation of transcription, N-terminal proteinmyristoylation, response to oxidative stress, cellular component, leafsenescence, resistance gene-dependent defense response signalingpathway, zinc ion binding, response to cold, malate metabolic process,transport, catalytic activity, response to ozone, VQ motif, regulationof systemic acquired resistance, potassium ion transport, anaerobicrespiration, multicellular organismal development, response to heat,methyltransferase activity, response to wounding, oxidation-reductionprocess, monooxygenase activity, oxidation-reduction process,carbohydrate metabolic process, exocytosis, nuclear-transcribed mRNApoly(A) tail shortening, sodium ion transport, glycerol metabolicprocess, on willebrand factor A3, response to water deprivation,response to salt stress, and chlorophyll biosynthetic process. In someembodiments, the gene has a gene ontology (GO) identifier selected fromthe group consisting of: GO:0003824, GO, catalytic activity; GO:0006355,GO, regulation of transcription, DNA-dependent; GO:0009870, GO, defenseresponse signaling pathway, resistance gene-dependent; GO:0008150, GO,biological process; GO:0010200, GO, response to chitin; GO:0006508, GO,proteolysis; GO:0010193, GO, response to ozone; GO:0006979, GO, responseto oxidative stress; and GO:0005975, GO, carbohydrate metabolic process.

In some embodiments, the gene function is selected from the followinggroup: single-stranded DNA specific endodeoxyribonuclease activity,sequence-specific DNA binding transcription factor activity,NAD+ADP-ribosyltransferase activity, metalloendopeptidase activity, DNAcatabolic process, cellular iron ion homeostasis, response to osmoticstress, metallopeptidase activity, zinc ion binding, response towounding, camalexin biosynthetic process, endoribonuclease activity,producing 5′-phosphomonoesters, cellular response to heat, T/Gmismatch-specific endonuclease activity, polyamine oxidase activity,flavin adenine dinucleotide binding, cellular heat acclimation, cellularresponse to ethylene stimulus, cellular response to nitric oxide, andreactive oxygen species metabolic process.

In some embodiments, the endophyte comprises an ITS rRNA nucleic acidsequence at least 95%, at least 96%, at least 97%, at least 98%, atleast 99%, or 100% identical to the nucleic acid sequence of SEQ ID NO:344.

In some embodiments of any of the plants, formulations, syntheticcombinations, or other compositions of the invention, the endophyteexpresses one or more genes encoding a protein whose amino acid sequenceis at least 95%, at least 96%, at least 97%, at least 98%, at least 99%,or 100% identical to an amino acid sequence selected from the groupconsisting of SEQ ID NOs: 477-501, 505, 514, 518, 521, 528, 530, 531,550, 566, 567, 572, 579, 580, 581, 587, 593, 600, 602, 614, 623, 630,635, 643, 645, 652, 657, 661, 662, 667, 670, 672, 673, 4510-4535, 4540,4541, 4542, 4547, 4555, 4558, 4560, 4569, 4570, 4571, 4572, 4577, 4582,4592, 4594, 4602, 4608, 4609, 4622, 4626, 4641, 4643, 4653, 4654,4742-4766, 4734, 4739, 4740, 477, 478, 480, 482, 484, 485, 487, 489,494, 496, 497, 501, 530, 567, 587, 602, 614, 633, 645, 649, 651, 652,658, 665, 666, 667, 673, 874, 934, 1013, 1249, 1342, 2252, 2272, 2273,2281, 2282, 2284, 2285, 2286, 2287, 2289, 2290, 2291, 2292, 2293, 2296,4510, 4514, 4515, 4518, 4520, 4521, 4525, 4526, 4527, 4529, 4532, 4538,4539, 4540, 4555, 4559, 4560, 4562, 4569, 4570, 4571, 4572, 4577, 4581,4582, 4594, 4595, 4597, 4608, 4615, 4618, 4623, 4624, 4626, 4630, 4632,4635, 4641, 4642, 4646, 4650, 4658, 4659, 4661, 4662, 4663, 4666, 4667,4668, 4670, 4799, 4801, 4802, 4803, 4804, 4805, 4826, 4827, 4828, 4829,4830, 4831, 4832, 4833, 4834, 4835, 4836, 4837, 4838, 4839, 4840, 4841,4863, 4864, 4865, 4866, 4867, 4868, 4869, 4870, 4871, 4872, 4873, 4874,4875, 4876, 4877, 4878, 4879, 4880, 4881, 4882, 4883, 4884, 4885, 4886,4887, 4888, 4889, 4890, 4891, 4892, 4893, 4894, 4917, 4918, 4919, 4920,4921, 4922, 4923, 4924, 4925, 4939, 4940, 4941, 4943, 4947, 4948, 4950,4951, 4955, 4956, 4957, 2315, 2320, 2322, 2326, 2349, 2350, 2352, 2377,2382, 2390, 2407, 2422, 2436, 2443, 2457, 2463, 2464, 2470, 2477, 2483,2721, 2968, 3093, 3185, 4096, 4097, 4098, 4099, 4100, 4101, 4102, 4103,4104, 4105, 4106, 4107, 4108, 4109, 4110, 4111, 4112, 4113, 4114, 4115,4116, 4117, 4118, 4119, 4120, 4121, 4122, 4123, 4124, 4125, 4126, 4346,4353, 4362, 4369, 4386, 4391, 4394, 4408, 4410, 4413, 4415, 4422, 4423,4432, 4433, 4442, 4469, 4487, 4489, 4491, 4493, 4494, 4495, 4496, 4497,4498, 4499, 4500, 4501, 4502, 4503, 4504, 4505, 4506, 4507, 4508, 4509,4343, 4484, 4485, 4486, 4488, 4490, and 4492.

In some embodiments of any of the plants, formulations, syntheticcombinations, or other compositions of the invention, the endophyteexpresses one or more genes involved in starch and sucrose metabolism,cell wall degradation, or protection from oxidative stress. In someembodiments, the protein is expressed with at least a two-folddifference, at least a three-fold difference, at least a four-folddifference, at least a five-fold difference, at least a six-folddifference, at least a seven-fold difference, at least an eight-folddifference, at least a nine-fold difference, at least a ten-folddifference or more in expression level as compared to the proteinexpression level of a reference microorganism. In some embodiments, thedifference in expression level is positive.

In some embodiments, the difference in expression level is negative. Insome embodiments, the endophyte comprises an ITS rRNA nucleic acidsequence at least 95%, at least 96%, at least 97%, at least 98%, atleast 99%, or 100% identical to a nucleic acid sequence selected fromthe group consisting of SEQ ID NOs: 344 and 447. In some embodiments,the wherein the endophyte comprises a 16S rRNA nucleic acid sequence atleast 95%, at least 96%, at least 97%, at least 98%, at least 99%, or100% identical to a nucleic acid sequence selected from the groupconsisting of SEQ ID NOs: 439 or 441.

Therefore, in a first aspect, inventions described herein provide asynthetic combination of a plant element of a first plant and apreparation of an endophyte that is coated onto the surface of the plantelement of the first plant such that the endophyte is present at ahigher level on the surface of the plant element than is present on thesurface of an uncoated reference plant element, wherein the endophyte isisolated from the inside of the plant element of a second plant. In someembodiments, a synthetic combination comprises a plant element of afirst plant and a preparation of one or more endophytes. In someembodiments, the one or more endophytes are selected from the groupconsisting of fungi, bacteria, and combinations thereof. In someembodiments, the one or more endophytes of the synthetic combination arefungi. In some embodiments, at least 1, 2, 3, 4, 5, 6, 7, 8, 9 or 10 ormore endophytes of the synthetic combination are fungi. In someembodiments, one or more endophytes of the synthetic combination arebacteria. In some embodiments, at least 1, 2, 3, 4, 5, 6, 7, 8, 9 or 10or more endophytes of the synthetic combination are bacteria. In someembodiments, one or more endophytes of the synthetic combinationcomprise both fungi and bacteria. In some embodiments, one or moreendophytes of the synthetic combination comprise at least one fungus andat least one bacterium. In some embodiments, one or more endophytes ofthe synthetic combination comprise at least 1, 2, 3, 4, 5, 6, 7, 8, 9 or10 or more bacteria, at least 1, 2, 3, 4, 5, 6, 7, 8, 9 or 10 or morefungi, and combinations thereof.

In some embodiments, the endophyte comprises a taxon that is present inat least two species that are selected from cereal, fruit and vegetable,wild grassland and oilseed plants. In some embodiments, the endophytecomprises a nucleic acid that is at least 97% identical, for example, atleast 98% identical, at least 99% identical, at least 99.5% identical,or 100% identical to the nucleic acid sequence selected from the groupsprovided in Table 1, Table 2, Table 7, and Table 8.

In some embodiments, the isolated endophyte is cultured, for example,prior to being coated onto the surface of the plant element. Theendophyte can be cultured in a synthetic or semi-synthetic medium.

The isolated endophyte can be associated with the surface of the seed ofthe first plant. In some embodiments, the endophyte is not associatedwith the surface of the plant element of the first plant.

The present invention contemplates a synthetic combination in which thefirst plant and the second plant are the same species. In a particularembodiment, the first plant and the second plant are the same cultivar.The synthetic combination may also make use of an endophyte that isisolated from a plant that is a different species from the first plant.

In some embodiments, the plant element of the first plant is from amonocotyledonous plant. For example, the plant element of the firstplant is from a cereal plant. The plant element of the first plant canbe selected from the group consisting of maize, wheat, barley, onion,rice, or sorghum. In an alternative embodiment, the seed of the firstplant is from a dicotyledonous plant. The plant element of the firstplant can be selected from the group consisting of cotton, Brassicanapus, tomato, pepper, cabbage, lettuce, melon, strawberry, turnip,watermelon, peanut or soybean. In a particular embodiment, the plant isnot a cotton plant. In still another embodiment, the plant is not asoybean. In another embodiment, the plant is not maize. In yet anotherembodiment, the plant is not wheat.

In some embodiments, the plant element of the first plant can be from agenetically modified plant. In another embodiment, the plant element ofthe first plant can be a hybrid plant element.

The synthetic combination can comprise a plant element of the firstplant that is surface-sterilized prior to combining with the endophytes.

As stated above, the endophyte used in the synthetic combination isderived from within the plant element of a second plant. In someembodiments, the second plant is a monocotyledonous plant or tissuethereof. In a particular embodiment, the second plant is a cereal plantor tissue thereof. In some embodiments, the second plant is selectedfrom the group consisting of a maize plant, a barley plant, a wheatplant, an onion plant, a rice plant, or a sorghum plant. In someembodiments, the plant element is a seed that is a naked grain (i.e.,without hulls or fruit cases). In an alternative embodiment, the secondplant is a dicotyledonous plant. For example, the second plant can beselected from the group consisting of a cotton plant, a Brassica Napusplant, a tomato plant, a pepper plant, a cabbage plant, a lettuce plant,a melon plant, a strawberry plant, a turnip plant, a watermelon plant, apeanut plant or a soybean plant.

In some embodiments, the endophyte is coated on the surface of the plantelement of the first plant in an amount effective to confer in the plantelement or resulting plant thereof an improved agronomic trait. Forexample, in one embodiment, the agronomic trait is selected from thegroup consisting of: improved leaf biomass, improved vigor, improvedfruit mass, improved grain yield, improved root mass, increased flowernumber, increased plant height, earlier flowering, and enhancedgermination rate. Alternatively, or in addition, the agronomic trait isselected from the group consisting of: improved resistance to drought,improved water use efficiency, improved nitrogen use efficiency,improved nitrogen uptake, improved resistance to salt stress, improvedresistance to heat, improved resistance to cold, improved metaltolerance, and improved nutritional content, improved uptake ofmicronutrients including metal ions, improved uptake of phosphorus andimproved uptake of potassium. In some embodiments, the agronomic traitis selected from the group consisting of: improved nematode resistance,improved fungal pathogen resistance, improved pathogen resistance,improved herbivore resistance, improved viral pathogen resistance.

In some embodiments, the seed of the first plant is coated with at least1 CFU or spores of the endophyte per seed, for example, at least 2 CFUor spores, at least 5 CFU or spores, at least 10 CFU or spores, at least30 CFU or spores, at least 100 CFU or spores, at least 300 CFU orspores, at least 1,000 CFU or spores, at least 3,000 CFU or spores, atleast 10,000 CFU or spores, at least 30,000 CFU or spores or more perseed.

The synthetic combination can additionally comprise a seed coatingcomposition. The seed coating composition can comprise an agent selectedfrom the group consisting of: a fungicide, an antibacterial agent, anherbicide, a nematicide, an insecticide, a plant growth regulator, arodenticide, a nutrient, and combinations thereof. The seed coatingcomposition can further comprise an agent selected from the groupconsisting of an agriculturally acceptable carrier, a tackifier, amicrobial stabilizer, and combinations thereof. In some embodiments, theseed coating composition can contain a second microbial preparation,including but not limited to a rhizobial bacterial preparation.

The present invention contemplates the use of endophytes that areunmodified, as well as those that are modified. In some embodiments, theendophyte is a recombinant endophyte. In one particular embodiment, theendophyte is modified prior to coating onto the surface of the seed suchthat it has enhanced compatibility with an antimicrobial agent whencompared with the unmodified. For example, the endophyte can be modifiedsuch that it has enhanced compatibility with an antibacterial agent. Inan alternative embodiment, the endophyte has enhanced compatibility withan antifungal agent. The endophyte can be modified such that it exhibitsat least 3 fold greater, for example, at least 5 fold greater, at least10 fold greater, at least 20 fold greater, at least 30 fold greater ormore resistance to an antimicrobial agent when compared with theunmodified endophyte. The endophyte can be substantially purified fromany other microbial entity. In one embodiment, the antimicrobial agentis an antibacterial agent. In another embodiment, the antimicrobialagent is an antifungal agent.

In one particular embodiment, the antimicrobial agent is glyphosate. Forexample, the modified endophyte exhibits at least 3 fold greater, forexample, at least 5 fold greater, at least 10 fold greater, at least 20fold greater, at least 30 fold greater or more resistance to theantimicrobial agent when compared with the unmodified endophyte. In thealternative, the modified endophyte has a doubling time in growth mediumcontaining at least 1 mM glyphosate, for example, at least 2 mMglyphosate, at least 5 mM glyphosate, at least 10 mM glyphosate, atleast 15 mM glyphosate or more, that is no more than 250%, for example,no more than 200%, no more than 175%, no more than 150%, or no more than125%, of the doubling time of the endophyte in the same growth mediumcontaining no glyphosate. In still another embodiment, the modifiedendophyte has a doubling time in a plant tissue containing at least 10ppm glyphosate, for example, at least 15 ppm glyphosate, at least 20 ppmglyphosate, at least 30 ppm glyphosate, at least 40 ppm glyphosate ormore, that is no more than 250%, for example, no more than 200%, no morethan 175%, no more than 150%, or no more than 125%, of the doubling timeof the unmodified endophyte in a reference plant tissue containing noglyphosate.

The present invention also contemplates the use of multiple endophytes.For example, in some embodiments, the synthetic combination describedabove can comprise a plurality of purified endophytes, for example, 2,3, 4 or more different types of endophytes.

In another aspect, the present invention provides for a method forimproving a trait in an agricultural plant, the method comprising:Providing an agricultural plant, contacting the plant with a formulationcomprising a endophytic microbial entity comprising a nucleic acidsequence that is at least 97% identical, at least 98% identical, atleast 99% identical, at least 99.5% identical, or 100% identical, to thenucleic acid sequence selected from the groups provided in Table 1,Table 2, Table 7, and Table 8 that is present in the formulation in anamount effective to colonize the plant and allowing the plant to growunder conditions that allow the endophytic microbial entity to colonizethe plant.

Also described herein are preparations comprising a population ofisolated modified endophytes described above. Preparations describedherein further comprise an agriculturally acceptable carrier, and thepreparation comprises an amount of endophytes sufficient to improve anagronomic trait of the population of seeds. For example, in oneembodiment, the agronomic trait is selected from the group consistingof: improved leaf biomass, improved vigor, improved fruit mass, improvedgrain yield, improved root mass, increased flower number, increasedplant height, earlier flowering, enhanced germination rate andcombinations thereof. Alternatively, or in addition, the agronomic traitis selected from the group consisting of: improved resistance todrought, improved water use efficiency, improved nitrogen useefficiency, improved nitrogen uptake, improved resistance to saltstress, improved resistance to heat, improved resistance to cold,improved metal tolerance, improved nutritional content, improved uptakeof micronutrients including metal ions, improved uptake of phosphorus,improved uptake of potassium and combinations thereof. In someembodiments, the agronomic trait is selected from the group consistingof: improved nematode resistance, improved fungal pathogen resistance,improved pathogen resistance, improved herbivore resistance, improvedviral pathogen resistance, and combinations thereof. In someembodiments, the preparation is substantially stable at temperaturesbetween about 2° C. and about 45° C. for at least about thirty days.

Preparations can be conveniently formulated to provide the ideal numberof endophytes onto a seed to produce synthetic combinations describedabove. In some embodiments, a preparation is formulated to provide atleast 100 endophytes, for example, at least 300 endophyte, 1,000endophytes, 3,000 endophytes, 10,000 endophytes or more per seed. Insome embodiments, a preparation is formulated to provide a population ofplants that demonstrates a substantially homogenous growth rate whenintroduced into agricultural production. Inventions described hereinalso contemplate a preparation comprising two or more different purifiedendophytes.

Also described herein are commodity plant products comprising a plant orpart of a plant (including a seed) and further comprising the modifiedendophyte described above that is present in a detectable level, forexample, as detected by the presence of its nucleic acid by PCR.

In another aspect of the present invention, a seed comprising syntheticcombinations described herein is provided. In still another aspect,disclosed is a substantially uniform population of seeds comprising aplurality of such seeds. In one embodiment, at least 10%, at least 20%,at least 30%, at least 40%, at least 50%, at least 60%, at least 70%, atleast 75%, at least 80%, at least 90%, at least 95% or more of the seedsin the population, contains a viable endophyte or endophytes disposed onthe surface of the seeds. In a particular embodiment, at least 10%, atleast 20%, at least 30%, at least 40%, at least 50%, at least 60%, atleast 70%, at least 75%, at least 80%, at least 90%, at least 95% ormore of the seeds in the population contains at least 10 CFU or spores,for example, at least 30 CFU or spores, at least 100 CFU or spores, atleast 300 CFU or spores, at least 1,000 CFU or spores, at least 3,000CFU or spores, at least 10,000 CFU or spores or more, of the endophyteor endophytes coated onto the surface of the seed.

In still another aspect, the present invention discloses a substantiallyuniform population of plants produced by growing the population of seedsdescribed above. In one embodiment, at least 75%, at least 80%, at least90%, at least 95% or more of the plants comprise in one or more tissuesan effective amount of the endophyte or endophytes. In anotherembodiment, at least 10%, 20%, 30%, 40%, 50%, 60%, 70%, 75%, at least80%, at least 90%, at least 95% or more of the plants comprise a microbepopulation that is substantially similar.

In another aspect, described herein is an agricultural field, includinga greenhouse comprising the population of plants described above. In onembodiment, the agricultural field comprises at least 100 plants. Inanother embodiment, the population occupies at least about 100 squarefeet of space, wherein at least about 10%, 20%, 30%, 40%, 50%, 60%, 70%,80%, 90% or more than 90% of the population comprises an effectiveamount of the microbe. In another embodiment, the population occupies atleast about 100 square feet of space, wherein at least about 10%, 20%,30%, 40%, 50%, 60%, 70%, 80%, 90% or more than 90% of the populationcomprises the microbe in reproductive tissue. In still anotherembodiment, the population occupies at least about 100 square feet ofspace, wherein at least about 10%, 20%, 30%, 40%, 50%, 60%, 70%, 80%,90% or more than 90% of the population comprises at least 10 CFUs orspores, 100 CFUs or spores, 1,000 CFUs or spores, 10,000 CFUs or sporesor more of the microbe. In yet another embodiment, the populationoccupies at least about 100 square feet of space, wherein at least about10%, 20%, 30%, 40%, 50%, 60%, 70%, 80%, 90% or more than 90% of thepopulation comprises an exogenous microbe (i.e., the endophyte) ofmonoclonal origin.

In another aspect, disclosed is a method of producing a commodity plantproduct, comprising obtaining a plant or plant tissue from the syntheticcombination described above, and producing the commodity plant producttherefrom. The commodity plant product can be produced from the seed, orthe plant (or a part of the plant) grown from the seed. The commodityplant product can also be produced from the progeny of such plant orplant part. The commodity plant product can be is selected from thegroup consisting of grain, flour, starch, seed oil, syrup, meal, flour,oil, film, packaging, nutraceutical product, an animal feed, a fishfodder, a cereal product, a processed human-food product, a sugar or analcohol and protein.

BRIEF DESCRIPTION OF THE DRAWINGS

The drawings are for illustration purposes only not for limitation.

FIG. 1 depicts an exemplary schematic of a KEGG pathway forGlycolysis/Gluconeogenesis. The secreted proteome of a beneficial andneutral Agrobacterium were contrasted, and KEGG IDs that were enrichedare depicted. 5AY represents beneficial SYM01004 (SEQ ID NO: 441). 5BYrepresents neutral SYM00091 (SEQ ID NO: 427). Light grey ovals representproteins corresponding to 5AY. Dark grey ovals represent proteinscorresponding to 5BY. Medium grey ovals represent proteins correspondingwith both 5AY and 5BY. P-value=1.36e-8

FIG. 2 depicts an exemplary schematic of a KEGG pathway for starch andsucrose metabolism. The secreted proteome of a beneficial and neutralbacteria and fungi were contrasted, and KEGG IDs that were enriched aredepicted.

DETAILED DESCRIPTION Definitions

In order for the present invention to be more readily understood,certain terms are first defined below. Additional definitions for thefollowing terms and other terms are set forth throughout thespecification.

As used herein, an “agricultural seed” is a seed used to grow a planttypically used in agriculture (an “agricultural plant”). The seed may beof a monocot or dicot plant, and may be planted for the production of anagricultural product, for example grain, food, feed, fiber, fuel, etc.As used herein, an agricultural seed is a seed that is prepared forplanting, for example, in farms for growing.

An “endophyte” or “endophytic entity” or “endophytic microbe” is asymbiotic organism (e.g., a microorganism, e.g., a bacterium, e.g., afungi) capable of living within a plant or is otherwise associatedtherewith, and does not cause disease or harm the plant otherwise, andconfers one or more beneficial properties to the host plant. In someembodiments, an endophyte is a microorganism. In some embodiments, anendophyte is a microorganism that is associated with one or more hostplant tissues and is in a symbiotic, e.g., beneficial relationship withsaid host plant tissues. In some embodiments, an endophyte is amicroorganism, e.g., a bacterial or fungal organism, that confers anincrease in yield, an increase in biomass, an increase in stressresistance, an increase in fitness, or combinations thereof, in its hostplant. Endophytes may occupy the intracellular or extracellular spacesof plant tissue, including the leaves, stems, flowers, fruits, seeds,roots and combinations thereof. As used herein, the term “endophyticcomponent” refers to a composition and/or structure that is part of theendophyte.

As used herein, the term “microbe” or “microorganism” refers to anyspecies or taxon of microorganism, including, but not limited to,archaea, bacteria, microalgae, fungi (including mold and yeast species),mycoplasmas, microspores, nanobacteria, oomycetes, and protozoa. In someembodiments, a microbe or microorganism is an endophyte. In someembodiments, a microbe is an endophyte. In some embodiments, a microbeor microorganism encompasses individual cells (e.g., unicellularmicroorganisms) or more than one cell (e.g., multi-cellularmicroorganism). A “population of microorganisms” may thus refer to amultiple cells of a single microorganism, in which the cells sharecommon genetic derivation. As used herein, the term “neutral” microbe or“neutral” microorganism refers to a microorganism that is bothnon-beneficial and non-pathogenic to a host plant.

As used herein, the term “bacteria” or “bacterium” refers in general toany prokaryotic organism, and may reference an organism from eitherKingdom Eubacteria (Bacteria), Kingdom Archaebacteria (Archae), or both.

As used herein, the term “fungus” or “fungi” refers in general to anyorganism from Kingdom Fungi.

A “spore” or a population of “spores” refers to bacteria or fungi thatare generally viable, more resistant to environmental influences such asheat and bactericidal or fungicidal agents than other forms of the samebacteria or fungi, and typically capable of germination and out-growth.Bacteria and fungi that are “capable of forming spores” are thosebacteria and fungi comprising the genes and other necessary abilities toproduce spores under suitable environmental conditions.

“Internal Transcribed Spacer” (ITS) refers to the spacer DNA (non-codingDNA) situated between the small-subunit ribosomal RNA (rRNA) andlarge-subunit rRNA genes in the chromosome or the correspondingtranscribed region in the polycistronic rRNA precursor transcript.

A “plurality of endophytes” means two or more types of endophyteentities, e.g., of simple bacteria or simple fungi, complex fungi, orcombinations thereof. In some embodiments, the two or more types ofendophyte entities are two or more strains of endophytes. In otherembodiments, the two or more types of endophyte entities are two or morespecies of endophytes. In yet other embodiments, the two or more typesof endophyte entities are two or more genera of endophytes. In yet otherembodiments, the two or more types of endophyte entities are two or morefamilies of endophytes. In yet other embodiments, the two or more typesof endophyte entities are two or more orders of endophytes.

A “population” of endophytes refers to a plurality of cells of a singleendophyte, in which the cells share common genetic derivation.

A “complex network” means a plurality of endophytes co-localized in anenvironment, such as on or within an agricultural plant. Preferably, acomplex network includes two or more types of endophyte entities thatsynergistically interact, such synergistic endophytic populationscapable of providing a benefit to the agricultural seed, seedling, orplant derived thereby.

The terms “pathogen” and “pathogenic” in reference to a bacterium orfungus includes any such organism that is capable of causing oraffecting a disease, disorder or condition of a host comprising theorganism.

A “spore” or a population of “spores” refers to bacteria or fungi thatare generally viable, more resistant to environmental influences such asheat and bactericidal or fungicidal agents than other forms of the samebacteria or fungi, and typically capable of germination and out-growth.Bacteria and fungi that are “capable of forming spores” are thosebacteria and fungi comprising the genes and other necessary abilities toproduce spores under suitable environmental conditions.

As used herein, a “colony-forming unit” (“CFU”) is used as a measure ofviable microorganisms in a sample. A CFU is an individual viable cellcapable of forming on a solid medium a visible colony whose individualcells are derived by cell division from one parental cell.

The term “isolated” is intended to specifically reference an organism,cell, tissue, polynucleotide, or polypeptide that is removed from itsoriginal source and purified from additional components with which itwas originally associated. For example, an endophyte may be consideredisolated from a seed if it is removed from that seed source and purifiedso that it is isolated from any additional components with which it wasoriginally associated. Similarly, an endophyte may be removed andpurified from a plant or plant element so that it is isolated and nolonger associated with its source plant or plant element.

As used herein, an isolated strain of a microbe is a strain that hasbeen removed from its natural milieu. “Pure cultures” or “isolatedcultures” are cultures in which the organisms present are only of onestrain of a particular genus and species. This is in contrast to “mixedcultures,” which are cultures in which more than one genus and/orspecies of microorganism are present. As such, the term “isolated” doesnot necessarily reflect the extent to which the microbe has beenpurified. A “substantially pure culture” of the strain of microbe refersto a culture which contains substantially no other microbes than thedesired strain or strains of microbe. In other words, a substantiallypure culture of a strain of microbe is substantially free of othercontaminants, which can include microbial contaminants. Further, as usedherein, a “biologically pure” strain is intended to mean the strainseparated from materials with which it is normally associated in nature.A strain associated with other strains, or with compounds or materialsthat it is not normally wound with in nature, is still defined as“biologically pure.” A monoculture of a particular strain is, of course,“biologically pure.” As used herein, the term “enriched culture” of anisolated microbial strain refers to a microbial culture that containsmore that 50%, 60%, 70%, 80%, 90%, or 95% of the isolated strain.

A “plant element” is intended to generically reference either a wholeplant or a plant component, including but not limited to plant tissues,parts, and cell types. A plant element is preferably one of thefollowing: whole plant, seedling, meristematic tissue, ground tissue,vascular tissue, dermal tissue, seed, leaf, root, shoot, stem, flower,fruit, stolon, bulb, tuber, corm, kelkis, shoot, bud. As used herein, a“plant element” is synonymous to a “portion” of a plant, and refers toany part of the plant, and can include distinct tissues and/or organs,and may be used interchangeably with the term “tissue” throughout.

Similarly, a “plant reproductive element” is intended to genericallyreference any part of a plant that is able to initiate other plants viaeither sexual or asexual reproduction of that plant, for example but notlimited to: seed, seedling, root, shoot, stolon, bulb, tuber, corm,keikis, or bud.

A “population” of plants, as used herein, refers to a plurality ofplants that are of the same taxonomic category, typically of the samespecies, and will also typically share a common genetic derivation.

As used herein, an “agricultural seed” is a seed used to grow a planttypically used in agriculture (an “agricultural plant”). The seed may beof a monocot or dicot plant, and may be planted for the production of anagricultural product, for example feed, food, fiber, fuel, etc. As usedherein, an agricultural seed is a seed that is prepared for planting,for example, in farms for growing.

“Agricultural plants”, or “plants of agronomic importance”, includeplants that are cultivated by humans for food, feed, fiber, and fuelpurposes. Agricultural plants include monocotyledonous species such as:maize (Zea mays), common wheat (Triticum aestivum), spelt (Triticumspelta), einkorn wheat (Triticum monococcum), emmer wheat (Triticumdicoccum), durum wheat (Triticum durum), Asian rice (Oryza sativa),African rice (Oryza glabaerreima), wild rice (Zizania aquatica, Zizanialatifolia, Zizania palustris, Zizania texana), barley (Hordeum vulgare),Sorghum (Sorghum bicolor), Finger millet (Eleusine coracana), Prosomillet (Panicum miliaceum), Pearl millet (Pennisetum glaucum), Foxtailmillet (Setaria italica), Oat (Avena sativa), Triticale (Triticosecale),rye (Secale cereal), Russian wild rye (Psathyrostachys juncea), bamboo(Bambuseae), or sugarcane (e.g., Saccharum arundinaceum, Saccharumbarberi, Saccharum bengalense, Saccharum edule, Saccharum munja,Saccharum officinarum, Saccharum procerum, Saccharum ravennae, Saccharumrobustum, Saccharum sinense, or Saccharum spontaneum); as well asdicotyledonous species such as: soybean (Glycine max), canola andrapeseed cultivars (Brassica napus), cotton (genus Gossypium), alfalfa(Medicago sativa), cassava (genus Manihot), potato (Solanum tuberosum),tomato (Solanum lycopersicum), pea (Pisum sativum), chick pea (Cicerarietinum), lentil (Lens culinaris), flax (Linum usitatissimum), peanut(Arachis hypogaea) and many varieties of vegetables.

A “host plant” includes any plant, particularly a plant of agronomicimportance, which an endophyte can colonize. As used herein, anendophyte is said to “colonize” a plant or plant element when it can bestably detected within the plant or plant element over a period time,such as one or more days, weeks, months or years, in other words, acolonizing entity is not transiently associated with the plant or plantelement. Such host plants are preferably plants of agronomic importance.

A “non-host target” means an organism or chemical compound that isaltered in some way after contacting a host plant or host fungus thatcomprises an endophyte, as a result of a property conferred to the hostplant or host fungus by the endophyte.

As used herein, a “hybrid plant” refers generally refers to a plant thatis the product of a cross between two genetically different parentalplants. A hybrid plant is generated by either a natural or artificialprocess of hybridization whereby the entire genome of one species,variety cultivar, breeding line or individual plant is combined intra-or interspecifically into the genome of species, variety or cultivar orline, breeding line or individual plant by crossing.

An “inbred plant”, as used herein, refers to a plant or plant line thathas been repeatedly crossed or inbred to achieve a high degree ofgenetic uniformity, and low heterozygosity, as is known in the art.

The term “isoline” is a comparative term, and references organisms thatare genetically identical, but may differ in treatment. In one example,two genetically identical maize plant embryos may be separated into twodifferent groups, one receiving a treatment (such as transformation witha heterologous polynucleotide, to create a genetically modified plant)and one control that does not receive such treatment. Any phenotypicdifferences between the two groups may thus be attributed solely to thetreatment and not to any inherency of the plant's genetic makeup. Inanother example, two genetically identical seeds may be treated with aformulation that introduces an endophyte composition. Any phenotypicdifferences between the plants derived from those seeds may beattributed to the treatment, thus forming an isoline comparison.

Similarly, by the terms “reference plant”, “reference agriculturalplant” or “reference seed”, it is meant an agricultural plant or seed ofthe same species, strain, or cultivar to which a treatment, formulation,composition or endophyte preparation as described herein is notadministered/contacted. A reference agricultural plant or seed,therefore, is identical to the treated plant with the exception of thepresence of the endophyte and can serve as a control for detecting theeffects of the endophyte that is conferred to the plant.

A “reference environment” refers to the environment, treatment orcondition of the plant in which a measurement is made. For example,production of a compound in a plant associated with an endophyte can bemeasured in a reference environment of drought stress, and compared withthe levels of the compound in a reference agricultural plant under thesame conditions of drought stress. Alternatively, the levels of acompound in plant associated with an endophyte and referenceagricultural plant can be measured under identical conditions of nostress.

A “population” of plants refers to more than one plant, that are of thesame taxonomic categeory, typically be of the same species, and willalso typically share a common genetic derivation.

In some embodiments, the invention contemplates the use of microbes thatare “exogenous” to a seed or plant. As used herein, a microbe isconsidered exogenous to the seed or plant if the plant element that isunmodified (e.g., a plant element that is not treated with the pluralityof endophytes described herein) does not contain the microbe.

In some embodiments, a microbe can be “endogenous” to a seed or plant.As used herein, a microbe is considered “endogenous” to a plant or seed,if the endophyte or endophyte component is derived from, or is otherwisefound in, a plant element of the plant specimen from which it issourced. In embodiments in which an endogenous endophyte is applied, theendogenous microbe is applied in an amount that differs from the levelstypically found in the plant.

In some embodiments, the present invention contemplates the syntheticcompositions comprising the combination of a plant element, seedling, orwhole plants and an endophyte population, in which the endophytepopulation is “heterologously disposed”.

In some aspects, “heterologously disposed” means that the plant element,seedling, or plant does not contain detectable levels of the microbe inthat same plant element, seedling, or plant. For example if said plantelement or seedling or plant does not naturally have the endophyteassociated with it and the endophyte is applied, the endophyte would beconsidered to be heterologously disposed. In some aspects,“heterologously disposed” means that the endophyte is being applied to adifferent plant element than that with which the endophyte is naturallyassociated. For example, if said plant element or seedling or plant hasthe endophyte normally found in the root tissue but not in the leaftissue, and the endophyte is applied to the leaf, the endophyte would beconsidered to be heterologously disposed. In some aspects,“heterologously disposed” means that the endophyte being applied to adifferent tissue or cell layer of the plant element than that in whichthe microbe is naturally found. For example, if endophyte is naturallyfound in the mesophyll layer of leaf tissue but is being applied to theepithelial layer, the endophyte would be considered to be heterologouslydisposed. In some aspects, “heterologously disposed” means that theendophyte being applied is at a greater concentration, number, or amountof the plant element, seedling, or plant, than that which is naturallyfound in said plant element, seedling, or plant. For example, anendophyte concentration that is being applied is at least 1.5 times,between 1.5 and 2 times, 2 times, between 2 and 3 times, 3 times,between 3 and 5 times, 5 times, between 5 and 7 times, 7 times, between7 and 10 times, 10 times greater, or even greater than 10 times highernumber, amount, or concentration than that which is naturally present,the endophyte would be considered to be heterologously disposed. In someaspects, “heterologously disposed” means that the endophyte is appliedto a developmental stage of the plant element, seedling, or plant inwhich said endophyte is not naturally associated, but may be associatedat other stages. For example, if an endophyte is normally found at theflowering stage of a plant and no other stage, an endophyte applied atthe seedling stage may be considered to be heterologously disposed. Forthe avoidance of doubt, “heterologously disposed” contemplates use ofmicrobes that are “exogenous” to a seed or plant.

In some cases, the present invention contemplates the use of microbesthat are “compatible” with agricultural chemicals, including but notlimited to, a fungicide, an anti-complex compound, a bactericide, avirucide, an herbicide, a nematicide, a parasiticide, a pesticide, orany other agent widely used in agricultural which has the effect ofkilling or otherwise interfering with optimal growth of anotherorganism. As used herein, a microbe is “compatible” with an agriculturalchemical, when the microbe is modified, such as by genetic modification,e.g., contains a transgene that confers resistance to an herbicide, orotherwise adapted to grow in, or otherwise survive, the concentration ofthe agricultural chemical used in agriculture. For example, a microbedisposed on the surface of plant element is compatible with thefungicide metalaxyl if it is able to survive the concentrations that areapplied on the plant element surface.

“Biomass” means the total mass or weight (fresh or dry), at a giventime, of a plant tissue, plant tissues, an entire plant, or populationof plants, usually given as weight per unit area. The term may alsorefer to all the plants or species in the community (community biomass).

Some of the compositions and methods described herein involve singleendophyte strains or plurality of endophytes in an amount effective tocolonize a plant. As used herein, a microbe is said to “colonize” aplant or seed when it can exist in an endophytic relationship with theplant in the plant environment, for example inside the plant or a partor tissue thereof, including the seed.

The compositions and methods herein may provide for an improved“agronomic trait” or “trait of agronomic importance” to a host plant,which may include, but not be limited to, the following: altered oilcontent, altered protein content, altered seed carbohydrate composition,altered seed oil composition, and altered seed protein composition,chemical tolerance, cold tolerance, delayed senescence, diseaseresistance, drought tolerance, ear weight, growth improvement, healthenhancement, heat tolerance, herbicide tolerance, herbivore resistance,improved nitrogen fixation, improved nitrogen utilization, improved rootarchitecture, improved water use efficiency, increased biomass,increased root length, increased seed weight, increased shoot length,increased yield, increased yield under water-limited conditions, kernelmass, kernel moisture content, metal tolerance, number of ears, numberof kernels per ear, number of pods, nutrition enhancement, pathogenresistance, pest resistance, photosynthetic capability improvement,salinity tolerance, stay-green, vigor improvement, increased dry weightof mature seeds, increased fresh weight of mature seeds, increasednumber of mature seeds per plant, increased chlorophyll content,increased number of pods per plant, increased length of pods per plant,reduced number of wilted leaves per plant, reduced number of severelywilted leaves per plant, and increased number of non-wilted leaves perplant, a detectable modulation in the level of a metabolite, adetectable modulation in the level of a transcript, and a detectablemodulation in the proteome, compared to an isoline plant grown from aseed without said seed treatment formulation.

Additionally, “altered metabolic function” or “altered enzymaticfunction” may include, but not be limited to, the following: alteredproduction of an auxin, altered nitrogen fixation, altered production ofan antimicrobial compound, altered production of a siderophore, alteredmineral phosphate solubilization, altered production of a cellulase,altered production of a chitinase, altered production of a xylanase,altered production of acetoin and altered ability to metabolize a carbonsource.

An “increased yield” can refer to any increase in biomass or seed orfruit weight, seed size, seed number per plant, seed number per unitarea, bushels per acre, tons per acre, kilo per hectare, or carbohydrateyield. Typically, the particular characteristic is designated whenreferring to increased yield, e.g., increased grain yield or increasedseed size.

“Agronomic trait potential” is intended to mean a capability of a plantelement for exhibiting a phenotype, preferably an improved agronomictrait, at some point during its life cycle, or conveying said phenotypeto another plant element with which it is associated in the same plant.For example, a plant element may comprise an endophyte that will providebenefit to leaf tissue of a plant from which the plant element is grown;in such case, the plant element comprising such endophyte has theagronomic trait potential for a particular phenotype (for example,increased biomass in the plant) even if the seed itself does not displaysaid phenotype.

By the term “capable of metabolizing” a particular carbon substrate, itis meant that the endophyte is able to utilize that carbon substrate asan energy source.

The term “synthetic combination” means a plurality of elementsassociated by human endeavor, in which said association is not found innature. In some embodiments, “synthetic combination” is used to refer toa treatment formulation associated with a plant element. In some aspectsof the present invention, “synthetic combination” refers to a purifiedpopulation of endophytes in a treatment formulation comprisingadditional compositions with which said endophytes are not foundassociated in nature. The combination may be achieved, for example, bycoating the surface of the seed of a plant, such as an agriculturalplant, or host plant elements with an endophyte. In some embodiments ofthe present invention, “synthetic combination” refers to one or moreplant elements in association with an isolated, purified population ofendophytes in a treatment formulation comprising additional compositionswith which said endophytes are not found associated in nature.

A “treatment formulation” refers to a mixture of chemicals thatfacilitate the stability, storage, and/or application of the endophytecomposition(s). In some embodiments, an agriculturally compatiblecarrier can be used to formulate an agricultural formulation or othercomposition that includes a purified endophyte preparation. As usedherein an “agriculturally compatible carrier” refers to any material,other than water, that can be added to a plant element without causingor having an adverse effect on the plant element (e.g., reducing seedgermination) or the plant that grows from the plant element, or thelike.

In some cases, the present invention contemplates the use ofcompositions that are “compatible” with agricultural chemicals, forexample, a fungicide, an anti-complex compound, or any other agentwidely used in agricultural which has the effect of killing or otherwiseinterfering with optimal growth of another organism.

Some compositions described herein contemplate the use of anagriculturally compatible carrier. As used herein an “agriculturallycompatible carrier” is intended to refer to any material, other thanwater, which can be added to a seed or a seedling without causing/havingan adverse effect on the seed, the plant that grows from the seed, seedgermination, or the like.

As used herein, a nucleic acid has “homology” or is “homologous” to asecond nucleic acid if the nucleic acid sequence has a similar sequenceto the second nucleic acid sequence. The terms “identity”, “percentsequence identity” or “identical” in the context of nucleic acidsequences refer to the residues in the two sequences that are the samewhen aligned for maximum correspondence. There are a number of differentalgorithms known in the art that can be used to measure nucleotidesequence identity. For instance, polynucleotide sequences can becompared using FASTA, Gap or Bestfit, which are programs in WisconsinPackage Version 10.0, Genetics Computer Group (GCG), Madison, Wis. FASTAprovides alignments and percent sequence identity of the regions of thebest overlap between the query and search sequences. In someembodiments, sequences can be compared using Geneious (Biomatters, Ltd.,Auckland, New Zealand). In other embodiments, polynucleotide sequencescan be compared using the multiple sequence alignment algorithm MUSCLE.In some embodiments the nucleic acid sequence to be aligned is acomplete gene. In some embodiments, the nucleic acid sequence to bealigned is a gene fragment. In some embodiments, if the nucleic acidsequence to be aligned is a gene fragment, the percent identity to asecond nucleic acid sequence is considered X % identical if the twosequences are X % identical the length of the shortest sequence.

The term “substantial homology” or “substantial similarity,” whenreferring to a nucleic acid or fragment thereof, indicates that, whenoptimally aligned with appropriate nucleotide insertions or deletionswith another nucleic acid (or its complementary strand), there isnucleotide sequence identity in at least about 76%, 80%, 85%, or atleast about 90%, or at least about 95%, 96%, 97%, 98% or 99% of thenucleotide bases, as measured by any well-known algorithm of sequenceidentity, such as FASTA, BLAST, MUSCLE or Gap, as discussed above.

As used herein, the terms “operational taxonomic unit,” “OTU,” “taxon,”“hierarchical cluster,” and “cluster” are used interchangeably. Anoperational taxon unit (OTU) refers to a group of one or more organismsthat comprises a node in a clustering tree. The level of a cluster isdetermined by its hierarchical order. In some embodiments, an OTU is agroup tentatively assumed to be a valid taxon for purposes ofphylogenetic analysis. In other embodiments, an OTU is any of the extanttaxonomic units under study. In yet another embodiment, an OTU is givena name and a rank. For example, an OTU can represent a domain, asub-domain, a kingdom, a sub-kingdom, a phylum, a sub-phylum, a class, asub-class, an order, a sub-order, a family, a subfamily, a genus, asubgenus, or a species. In some embodiments, OTUs can represent one ormore organisms from the kingdoms eubacteria, protista, or fungi at anylevel of a hierarchal order. In some embodiments, an OTU represents aprokaryotic or fungal order.

As used herein, the terms “water-limited condition”, “water stresscondition” and “drought condition”, or “water-limited”, “water stress”,and “drought”, may be used interchangeably. For example, a method orcomposition for improving a plant's ability to grow under droughtconditions means the same as the ability to grow under water-limitedconditions. In such cases, the plant can be further said to displayimproved tolerance to drought stress.

The terms “decreased”, “fewer”, “slower” and “increased” “faster”“enhanced” “greater” as used herein refers to a decrease or increase ina characteristic of the endophyte treated seed or resulting plantcompared to an untreated seed or resulting plant. For example, adecrease in a characteristic may be at least 1%, at least 2%, at least3%, at least 4%, at least 5%, at least 10%, at least 15%, at least 20%,at least 25%, at least 30%, at least 35%, at least 40%, at least 45%, atleast 50%, at least about 60%, at least 75%, at least about 80%, atleast about 90%, at least 100%, at least 200%, at least about 300%, atleast about 400% or more lower than the untreated control. For example,a decrease may be between 1% and 5%, or between 5% and 10%, or between10% and 15%, or between 15% and 20%, or between 20% and 25%, or between25% and 30%, or between 30% and 35%, or between 35% and 40%, or between45% and 50% lower than the untreated control or the formulation control.An increase may be at least 1%, at least 2%, at least 3%, at least 4%,at least 5%, at least 10%, at least 15%, at least 20%, at least 25%, atleast 30%, at least 35%, at least 40%, at least 45%, at least 50%, atleast about 60%, at least 75%, at least about 80%, at least about 90%,at least 100%, at least 200%, at least about 300%, at least about 400%or more higher than the untreated control. For example, an increase maybe between 1% and 5%, or between 5% and 10%, or between 10% and 15%, orbetween 15% and 20%, or between 20% and 25%, or between 25% and 30%, orbetween 30% and 35%, or between 35% and 40%, or between 45% and 50%higher than the untreated control or the formulation control.

Endophytes

Agricultural plants appear to associate with symbiotic microorganismstermed endophytes, particularly bacteria and fungi, that may have beenimportant during evolution and may contribute to plant survival andperformance. However, modern agricultural processes may have perturbedthis relationship, resulting in increased crop losses, diminished stressresilience, biodiversity losses, and increasing dependence on externalchemicals, fertilizers, and other unsustainable agricultural practices.There is a need for novel methods for generating plants with novelmicrobiome properties that can sustainably increase yield, stressresilience, and decrease fertilizer and chemical use.

The inventors have undertaken a systematic comparison of the microbialcommunities that reside within a wide diversity of plants. As such, theendophytic microbes useful for the invention generally relate toendophytic microbes that are present in agricultural plants.

In part, the present invention describes preparations of novelendophytes, and the creation of synthetic combinations of agriculturalseeds and/or seedlings with heterologous endophytes and formulationscontaining the synthetic combinations, as well as the recognition thatsuch synthetic combinations display a diversity of beneficial propertiespresent in the agricultural plants and the associated endophytepopulations newly created by the present inventors. Such beneficialproperties include metabolism, transcript expression, proteomealterations, morphology, and the resilience to a variety ofenvironmental stresses, and the combination of a plurality of suchproperties.

Provided are novel compositions, methods, and products related ourinvention's ability to overcome the limitations of the prior art inorder to provide reliable increases in crop yield, biomass, germination,vigor, stress resilience, and other properties to agricultural crops.

We find that beneficial microbes can be robustly derived from plantelements, optionally cultured, administered heterologously toagricultural plant elements such as seeds, and colonize the resultingplant tissues with high efficiency to confer multiple beneficialproperties.

We find that microbes can confer beneficial properties across a range ofconcentrations.

We find that endophytes can be heterologously disposed onto seedlings ofa distinct cultivar, species, or crop type and confer benefits to thosenew recipients. For example, endophytes from corn cultivars areheterologously provided to wheat cultivars to confer a benefit. This issurprising given the observations of distinct microbiome preferences indistinct plant and mammalian hosts and, in particular, the likelihoodthat microbes derived from seeds have been co-evolved to be specializedto a particular host.

We further find that combinations of heterologously disposed endophytesconfer additive advantages to plants, including multiple functionalproperties and resulting in seed, seedling, and plant hosts that displaysingle or multiple improved agronomic properties.

Endophytes are microbes that grow inside a plant. Recent appreciationthat endophytes can confer remarkable traits upon the host plant is thebasis for the present invention. The inventors have developed a methodto introduce isolated endophytes to another plant by coating themicrobes onto the surface of a seed of a plant. By combining anendophyte sourced from one plant, it is possible to transfer thebeneficial agronomic trait onto an agricultural plant, and thereforeholds great promise for increasing agricultural productivity.

Combining a selected plant species, OTU, strain or cultivar with one ormore types of endophytes thus provides mechanisms by which, alone or inparallel with plant breeding and transgenic technologies, is providedimproved yield from crops and generation of products thereof. Therefore,in a first aspect, the present invention provides a syntheticcombination comprising the combination of a plant element, seedling, orwhole plants and a single endophyte strain or a plurality of endophytes,in which the single endophyte strain or a plurality of endophytes are“heterologously disposed.”

Synthetic Compositions of Plant Elements and Endophytes

The present invention contemplates a synthetic combination of a plantelement of a plant that is coated with an endophyte on its surface. Theplant element can be any agricultural plant element, for example anagricultural seed. In one embodiment, the plant element of the firstplant is from a monocotyledonous plant. For example, the plant elementof the first plant is from a cereal plant. The plant element of thefirst plant can be selected from the group consisting of a maize plant,a wheat plant, a barley plant, an onion plant, a sorghum plant, or arice plant. In an alternative embodiment, the plant element of the firstplant is from a dicotyledonous plant. The plant element of the firstplant can be selected from the group consisting of a cotton plant, aBrassica napus plant, a tomato plant, a pepper plant, a cabbage plant, alettuce plant, a melon plant, a strawberry plant, a turnip plant, awatermelon plant, a peanut plant, or a soybean plant. In a particularembodiment, the plant is not a cotton plant. In still anotherembodiment, the seed of the first plant can be from a geneticallymodified plant. In another embodiment, the seed of the first plant canbe a hybrid seed.

The synthetic combination can comprise a plant element of the firstplant that is surface-sterilized prior to combining with the endophytes.Such pre-treatment prior to coating the plant element with endophytesremoves the presence of other microbes that may interfere with theoptimal colonization, growth and/or function of the endophyte. Surfacesterilization of plant elements can be accomplished without killing theplant elements as described herein elsewhere (see, for example, thesection Isolation of endophytes).

Sources of Endophytes

As described herein, endophytes can be derived from heterologous,homologous, or engineered sources, optionally cultured, administeredheterologously as a single endophyte strain or a plurality of endophytesto plant elements, and, as a result of the administration, confermultiple beneficial properties. In some embodiments, endophytes arederived from plant elements or soil. In some embodiments, the plantelement from which the endophyte is derived is a monocotyledonous plant.In a particular embodiment, the plant is a cereal plant or tissuethereof. In yet another embodiment, plant is selected from the groupconsisting of a maize plant, a barley plant, a wheat plant, a sugarcaneplant, a sorghum plant, or a rice plant. In some embodiments, the plantelement is a naked grain (i.e., without hulls or fruit cases). In analternative embodiment, the plant element from which the endophyte isderived is a dicotyledonous plant. For example, a plant can be selectedfrom the group consisting of a cotton plant, a Brassica napus plant, atomato plant, a pepper plant, a cabbage plant, a lettuce plant, a melonplant, a strawberry plant, a turnip plant, a watermelon plant, a peanutplant, or a soybean plant.

In some embodiments, the endophytes can be obtained from a plant elementof the same or different crop, and can be from the same or differentcultivar or variety as the plant element to which the composition isheterologously associated. For example, endophytes from a particularcorn variety can be isolated and coated onto the surface of a corn seedof the same variety. In other embodiments, the endophytes can beisolated from a related species (e.g., an endophyte isolated fromTriticum monococcum (einkorn wheat) can be coated onto the surface of aT. aestivum (common wheat) plant element; or, an endophyte from Hordeumvulgare (barley) can be isolated and coated onto the plant element ofanother member of the Triticeae family, for example, plant elements ofthe rye plant, Secale cereale). In still another embodiment, theendophytes can be isolated from a plant part of a plant that isdistantly related to the plant element onto which the endophyte is to becoated. For example, tomato-derived endophytes are isolated and coatedonto a rice plant element. In still another embodiment, endophytes usedin a composition or used to make a synthetic composition can be obtainedfrom a plant element of a plant that is distantly related to the plantelement onto which the endophyte is to be coated. For example, atomato-derived endophyte can be isolated and coated onto a rice plantelement.

In some embodiments, the present invention contemplates the use ofendophytes that can confer a beneficial agronomic trait upon the seed orresulting plant onto which it is coated. In another embodiment, the seedendophytes useful for the present invention can also be isolated fromseeds of plants adapted to a particular environment, including, but notlimited to, an environment with water deficiency, salinity, acute and/orchronic heat stress, acute and/or chronic cold stress, nutrient deprivedsoils including, but not limited to, micronutrient deprived soils,macronutrient (e.g., potassium, phosphate, nitrogen) deprived soils,pathogen stress, including fungal, nematode, insect, viral, bacterialpathogen stress. In one example, the endophyte is isolated from the seedof a plant that grows in a water deficient environment.

The synthetic combination of the present invention contemplates thepresence of an endophyte on the surface of the seed of the first plant.In one embodiment, the seed of the first plant is coated with at least10 CFU or spores of the endophyte per seed, for example, at least 20 CFUor spores, at least 50 CFU or spores, at least 100 CFU or spores, atleast 200 CFU or spores, at least 300 CFU or spores, at least 500 CFU orspores, at least 1,000 CFU or spores, at least 3,000 CFU or spores, atleast 10,000 CFU or spores, at least 30,000 CFU or spores or more perplant element. In another embodiment, the plant element is coated withat least 10, for example, at least 20, at least 50, at least 100, atleast 200, at least 300, at least 500, at least 1,000, at least 3,000,at least 10,000, at least 30,000, at least 100,000, at least 300,000, atleast 1,000,000 or more of the endophyte as detected by the number ofcopies of a particular endophyte gene detected, for example, byquantitative PCR.

The endophyte useful for the present invention can be a fungus. Inanother embodiment, the endophyte can be a bacterium. In one embodiment,the endophyte is not an Agrobacterium. In another embodiment, theendophyte is not capable of nitrogen fixation (for example, from thegenus Rhizobium). In still another embodiment, the endophyte is not fromthe genus Acetobacter. In yet another embodiment, the endophyte is notfrom the genus Bacillus. In a particular embodiment, the endophyte isnot Bacillus mojavensis. In yet another embodiment, the endophyte is notfrom the genus Neotyphodium.

Historical taxonomic classification of fungi has been according tomorphological presentation. Beginning in the mid-1800's, it wasrecognized that some fungi have a pleomorphic life cycle, and thatdifferent nomenclature designations were being used for different formsof the same fungus. In 1981, the Sydney Congress of the InternationalMycological Association laid out rules for the naming of fungi accordingto their status as anamorph, teleomorph, or holomorph. With thedevelopment of genomic sequencing, it became evident that taxonomicclassification based on molecular phylogenetics did not align withmorphological-based nomenclature. As a result, in 2011 the InternationalBotanical Congress adopted a resolution approving the International Codeof Nomenclature for Algae, Fungi, and Plants (Melbourne Code) (2012),with the stated outcome of designating “One Fungus=One Name”. However,systematics experts have not aligned on common nomenclature for allfungi, nor are all existing databases and information resourcesinclusive of updated taxonomies. As such, many fungi referenced hereinmay be described by their anamorph form but it is understood that basedon identical genomic sequencing, any pleomorphic state of that fungusmay be considered to be the same organism. For example, the genusAlternaria is the anamorph form of the teleomorph genus Lewia, ergo bothwould be understood to be the same organism with the same DNA sequence.

Exogenous Endophytes

In one embodiment, the endophyte is an endophytic microbe that wasisolated from a different plant than the inoculated plant. For example,in one embodiment, the endophyte can be an endophyte isolated from adifferent plant of the same species as the inoculated plant. In somecases, the endophyte can be isolated from a species related to theinoculated plant.

The breeding of plants for agriculture, as well as cultural practicesused to combat microbial pathogens, may have resulted in the loss inmodern cultivars of the endophytes present in their wild ancestors orother wild plants, or such practices may have inadvertently promotedother novel or rare plant-endophyte interactions, or otherwise alteredthe microbial population. The former is the case in maize and itsphylogenetically confirmed, direct wild ancestor, Parviglumis teosinte(Zea mays ssp. Parviglumis). Although both species have seeds thatappear to contain a common core of endophytic bacterial species, therelative abundance of certain groups is higher in seeds of teosinte thanmodern corn. It is possible that this higher diversity and titer ofendophytes in the ancestor is correlated with an equally wide range ofphysiological responses derived from the symbiosis that allow the plantto better adapt to the environment and tolerate stress. In order tosurvey plant groups for potentially useful endophytes, seeds of theirwild ancestors, wild relatives, primitive landraces, modern landraces,modern breeding lines, and elite modern agronomic varieties can bescreened for microbial endophytes by culture and culture independentmethods as described herein. In addition, microbial endophytes can beisolated from other wild plants, such as grassland plants.

In some cases, plants are inoculated with endophytes that are exogenousto the seed of the inoculated plant. In one embodiment, the endophyte isderived from a plant of another species. For example, an endophyte thatis normally found in dicots is applied to a monocot plant (e.g.,inoculating corn with a soy bean-derived endophyte), or vice versa. Inother cases, the endophyte to be inoculated onto a plant can be derivedfrom a related species of the plant that is being inoculated. In oneembodiment, the endophyte can be derived from a related taxon, forexample, from a related species. The plant of another species can be anagricultural plant. For example, an endophyte derived from Hordeumirregulare can be used to inoculate a Hordeum vulgare L., plant.Alternatively, it can be derived from a ‘wild’ plant (i.e., anon-agricultural plant). For example, endophytes normally associatedwith the wild cotton Gossypium klotzschianum can be used to inoculatecommercial varieties of Gossypium hirsutum plants. Endophytes normallyassociated with a wild turnip plant or a wild watermelon plant can beused to inoculate commercial varieties of turnip or watermelon plants,respectively. As an alternative example of deriving an endophyte from a‘wild’ plant, endophytic bacteria isolated from the South East Asianjungle orchid, Cymbidium eburneum, can be isolated and testing for theircapacity to benefit seedling development and survival of agriculturalcrops such as wheat, maize, soy and others. In another example,endophytes may be isolated from wild grassland plants. In other cases,the endophyte can be isolated from an ancestral species of theinoculated plant. For example, an endophyte derived from Zeadiploperennis can be used to inoculate a commercial variety of moderncorn, or Zea mays.

Selection of Plant Species from Desired Habitats for Isolation ofMicrobial Endophytes

Different environments can contain significantly different populationsof endophytes. For example, geographically isolated soils from differentparts of the Americas have been shown to differ in 96% of the bacterialspecies they contain. Soils containing different microbial populationscan strongly influence the endophytic bacterial population observedinside Arabidopsis illustrating that the environment can at leastpartially alter a plant's associated microbial population. This suggeststhat plants growing and especially thriving in choice environments arecolonized by different and perhaps beneficial endophytes, whoseisolation and inoculation onto crop plants may aid these plants tobetter survive in the same choice environment or to better resistcertain stresses encountered in a normal agricultural environment. Forinstance, at least some of the bacteria isolated from plants growing inarid environments are expected to confer drought tolerance to hostplants they are transplanted onto. Additionally, novel endophtytes maybe found in related crop varieties grown in the choice environment. Oncea choice environment is selected, seeds of choice plants to be sampledwill be identified by their healthy and/or robust growth, and will thenbe sampled at least 5 at a time by excavating the entire plants plussmall root ball including roots and associated soil and any seeds orfruit present on the plant. These will be placed in a cool (4° C.environment) for storage and prompt transport back to the lab forextraction of endophytes and DNA using methods described herein.Identification of choice environments or ecosystems for bioprospectingof plant associated endophytes from either wild plants or crop plantsgrowing in the choice environments or ecosystems follows protocolsdescribed herein.

In one embodiment, the endophyte-associated plant is harvested from asoil type different than the normal soil type that the crop plant isgrown on, for example from a gelisol (soils with permafrost within 2 mof the surface), for example from a histosol (organic soil), for examplefrom a spodosol (acid forest soils with a subsurface accumulation ofmetal-humus complexes), for example from an andisol (soils formed involcanic ash), for example from a oxisol (intensely weathered soils oftropical and subtropical environments), for example from a vertisol(clayey soils with high shrink/swell capacity), for example from anaridisol (CaCO3-containing soils of arid environments with subsurfacehorizon development), for example from a ultisol (strongly leached soilswith a subsurface zone of clay accumulation and <35% base saturation),for example from a mollisol (grassland soils with high base status), forexample from an alfisol (moderately leached soils with a subsurface zoneof clay accumulation and >35% base saturation), for example from ainceptisol (soils with weakly developed subsurface horizons), forexample from a entisol (soils with little or no morphologicaldevelopment).

In another embodiment, the endophyte-associated plant is harvested froman ecosystem where the agricultural plant is not normally found, forexample a tundra ecosystem as opposed to a temperate agricultural farm,for example from tropical and subtropical moist broadleaf forests(tropical and subtropical, humid), for example from tropical andsubtropical dry broadleaf forests (tropical and subtropical, semihumid),for example from tropical and subtropical coniferous forests (tropicaland subtropical, semihumid), for example from temperate broadleaf andmixed forests (temperate, humid), for example from temperate coniferousforests (temperate, humid to semihumid), from for example from borealforests/taiga (subarctic, humid), for example from tropical andsubtropical grasslands, savannas, and shrublands (tropical andsubtropical, semiarid), for example from temperate grasslands, savannas,and shrublands (temperate, semiarid), for example from floodedgrasslands and savannas (temperate to tropical, fresh or brackish waterinundated), for example from montane grasslands and shrublands (alpineor montane climate), for example from Mediterranean forests, woodlands,and scrub or sclerophyll forests (temperate warm, semihumid to semiaridwith winter rainfall), for example from mangrove forests, and forexample from deserts and xeric shrublands (temperate to tropical, arid).

In another embodiment, the endophyte-associated plant is harvested froma soil with an average pH range that is different from the optimal soilpH range of the crop plant, for example the plant may be harvested froman ultra acidic soil (<3.5), from an extreme acid soil (3.5-4.4), from avery strong acid soil (4.5-5.0), from a strong acid soil (5.1-5.5), froma moderate acid soil (5.6-6.0), from an slight acid soil (6.1-6.5), froman neutral soil (6.6-7.3), from an slightly alkaline soil (7.4-7.8),from an moderately alkaline soil (7.9-8.4), from a strongly alkalinesoil (8.5-9.0), or from an very strongly alkaline soil (>9.0).

In one embodiment, the endophyte-associated plant is harvested from anenvironment with average air temperatures lower than the normal growingtemperature of the crop plant, for example 2-5° C. colder than average,for example, at least 5-10° C. colder, at least 10-15° C. colder, atleast at least 15-20° C. colder, at least 20-25° C. colder, at least25-30° C. colder, at least 30-35° C. colder, at least 35-40° C. colder,at least 40-45° C. colder, at least 45-50° C. colder, at least 50-55° C.colder or more, when compared with crop plants grown under normalconditions during an average growing season.

In one embodiment, the endophyte-associated plant is harvested from anenvironment with average air temperatures higher than the normal growingtemperature of the crop plant, for example 2-5° C. hotter than average,for example, at least 5-10° C. hotter, at least 10-15° C. hotter, atleast at least 15-20° C. hotter, at least 20-25° C. hotter, at least25-30° C. hotter, at least 30-35° C. hotter, at least 35-40° C. hotter,at least 40-45° C. hotter, at least 45-50° C. hotter, at least 50-55° C.hotter or more, when compared with crop plants grown under normalconditions during an average growing season.

In another embodiment, the endophyte-associated plant is harvested froman environment with average rainfall lower than the optimal averagerainfall received by the crop plant, for example 2-5% less rainfall thanaverage, for example, at least 5-10% less rainfall, at least 10-15% lessrainfall, at least 15-20% less rainfall, at least 20-25% less rainfall,at least 25-30% less rainfall, at least 30-35% less rainfall, at least35-40% less rainfall, at least 40-45% less rainfall, at least 45-50%less rainfall, at least 50-55% less rainfall, at least 55-60% lessrainfall, at least 60-65% less rainfall, at least 65-70% less rainfall,at least 70-75% less rainfall, at least 80-85% less rainfall, at least85-90% less rainfall, at least 90-95% less rainfall, or less, whencompared with crop plants grown under normal conditions during anaverage growing season.

In one embodiment, the endophyte-associated plant is harvested from anenvironment with average rainfall higher than the optimal averagerainfall of the crop plant, for example 2-5% more rainfall than average,for example, at least 5-10% more rainfall, at least 10-15% morerainfall, at least 15-20% more rainfall, at least 20-25% more rainfall,at least 25-30% more rainfall, at least 30-35% more rainfall, at least35-40% more rainfall, at least 40-45% more rainfall, at least 45-50%more rainfall, at least 50-55% more rainfall, at least 55-60% morerainfall, at least 60-65% more rainfall, at least 65-70% more rainfall,at least 70-75% more rainfall, at least 80-85% more rainfall, at least85-90% more rainfall, at least 90-95% more rainfall, at least 95-100%more rainfall, or even greater than 100% more rainfall, or even greaterthan 200% more rainfall, or even greater than 300% more rainfall, oreven greater than 400% more rainfall, or even greater than 500% morerainfall, when compared with crop plants grown under normal conditionsduring an average growing season.

In another embodiment, the endophyte-associated plant is harvested froma soil type with different soil moisture classification than the normalsoil type that the crop plant is grown on, for example from an aquicsoil (soil is saturated with water and virtually free of gaseous oxygenfor sufficient periods of time, such that there is evidence of pooraeration), for example from an udic soil (soil moisture is sufficientlyhigh year-round in most years to meet plant requirement), for examplefrom an ustic soil (soil moisture is intermediate between udic andaridic regimes; generally, plant-available moisture during the growingseason, but severe periods of drought may occur), for example from anaridic soil (soil is dry for at least half of the growing season andmoist for less than 90 consecutive days), for example from a xeric soil(soil moisture regime is found in Mediterranean-type climates, withcool, moist winters and warm, dry summers).

In one embodiment, the endophyte-associated plant is harvested from anenvironment with average rainfall lower than the optimal averagerainfall of the crop plant, for example 2-95% less rainfall thanaverage, for example, at least 5-90% less rainfall, at least 10-85% lessrainfall, at least 15-80% less rainfall, at least 20-75% less rainfall,at least 25-70% less rainfall, at least 30-65% less rainfall, at least35-60% less rainfall, at least 40-55% less rainfall, at least 45-50%less rainfall, when compared with crop plants grown under normalconditions during an average growing season.

In one embodiment, the endophyte-associated plant is harvested from anenvironment with average rainfall higher than the optimal averagerainfall of the crop plant, for example 2-5% more rainfall than average,for example, at least 5-10% more rainfall, at least 10-15% morerainfall, at least 15-20% more rainfall, at least 20-25% more rainfall,at least 25-30% more rainfall, at least 30-35% more rainfall, at least35-40% more rainfall, at least 40-45% more rainfall, at least 45-50%more rainfall, at least 50-55% more rainfall, at least 55-60% morerainfall, at least 60-65% more rainfall, at least 65-70% more rainfall,at least 70-75% more rainfall, at least 80-85% more rainfall, at least85-90% more rainfall, at least 90-95% more rainfall, at least 95-100%more rainfall, or even greater than 100% more rainfall, or even greaterthan 200% more rainfall, or even greater than 300% more rainfall, oreven greater than 400% more rainfall, or even greater than 500% morerainfall, when compared with crop plants grown under normal conditionsduring an average growing season.

In another embodiment, the endophyte-associated plant is harvested froman agricultural environment with a crop yield lower than the averagecrop yield expected from the crop plant grown under average cultivationpractices on normal agricultural land, for example 2-5% lower yield thanaverage, for example, at least 5-10% lower yield, at least 10-15% loweryield, at least 15-20% lower yield, at least 20-25% lower yield, atleast 25-30% lower yield, at least 30-35% lower yield, at least 35-40%lower yield, at least 40-45% lower yield, at least 45-50% lower yield,at least 50-55% lower yield, at least 55-60% lower yield, at least60-65% lower yield, at least 65-70% lower yield, at least 70-75% loweryield, at least 80-85% lower yield, at least 85-90% lower yield, atleast 90-95% lower yield, or less, when compared with crop plants grownunder normal conditions during an average growing season.

In a related embodiment, the endophyte-associated plant is harvestedfrom an agricultural environment with a crop yield lower than theaverage crop yield expected from the crop plant grown under averagecultivation practices on normal agricultural land, for example 2-95%lower yield than average, for example, at least 5-90% lower yield, atleast 10-85% lower yield, at least 15-80% lower yield, at least 20-75%lower yield, at least 25-70% lower yield, at least 30-65% lower yield,at least 35-60% lower yield, at least 40-55% lower yield, at least45-50% lower yield, when compared with crop plants grown under normalconditions during an average growing season.

In one embodiment, the endophyte-associated plant is harvested from anenvironment with average crop yield higher than the optimal average cropyield of the crop plant, for example 2-5% more yield than average, forexample, at least 5-10% more yield, at least 10-15% more yield, at least15-20% more yield, at least 20-25% more yield, at least 25-30% moreyield, at least 30-35% more yield, at least 35-40% more yield, at least40-45% more yield, at least 45-50% more yield, at least 50-55% moreyield, at least 55-60% more yield, at least 60-65% more yield, at least65-70% more yield, at least 70-75% more yield, at least 80-85% moreyield, at least 85-90% more yield, at least 90-95% more yield, at least95-100% more yield, or even greater than 100% more yield, or evengreater than 200% more yield, or even greater than 300% more yield, oreven greater than 400% more yield, or even greater than 500% more yield,when compared with crop plants grown under normal conditions during anaverage growing season.

In a related embodiment, the endophyte-associated plant is harvestedfrom an environment with average crop yield higher than the optimalaverage crop yield of the crop plant, 2-500% more yield than average,2-400% more yield than average, 2-300% more yield than average, 2-200%more yield than average, 2-95% more yield than average, for example, atleast 5-90% more yield, at least 10-85% more yield, at least 15-80% moreyield, at least 20-75% more yield, at least 25-70% more yield, at least30-65% more yield, at least 35-60% more yield, at least 40-55% moreyield, at least 45-50% more yield, when compared with crop plants grownunder normal conditions during an average growing season.

In another embodiment, the endophyte-associated plant is harvested froma environment where soil contains lower total nitrogen than the optimumlevels recommended in order to achieve average crop yields for a plantgrown under average cultivation practices on normal agricultural land,for example 2-5% less nitrogen than average, for example, at least 5-10%less nitrogen, at least 10-15% less nitrogen, at least 15-20% lessnitrogen, at least 20-25% less nitrogen, at least 25-30% less nitrogen,at least 30-35% less nitrogen, at least 35-40% less nitrogen, at least40-45% less nitrogen, at least 45-50% less nitrogen, at least 50-55%less nitrogen, at least 55-60% less nitrogen, at least 60-65% lessnitrogen, at least 65-70% less nitrogen, at least 70-75% less nitrogen,at least 80-85% less nitrogen, at least 85-90% less nitrogen, at least90-95% less nitrogen, or less, when compared with crop plants grownunder normal conditions during an average growing season.

In another embodiment, the endophyte-associated plant is harvested froma environment where soil contains higher total nitrogen than the optimumlevels recommended in order to achieve average crop yields for a plantgrown under average cultivation practices on normal agricultural land,for example 2-5% more nitrogen than average, for example, at least 5-10%more nitrogen, at least 10-15% more nitrogen, at least 15-20% morenitrogen, at least 20-25% more nitrogen, at least 25-30% more nitrogen,at least 30-35% more nitrogen, at least 35-40% more nitrogen, at least40-45% more nitrogen, at least 45-50% more nitrogen, at least 50-55%more nitrogen, at least 55-60% more nitrogen, at least 60-65% morenitrogen, at least 65-70% more nitrogen, at least 70-75% more nitrogen,at least 80-85% more nitrogen, at least 85-90% more nitrogen, at least90-95% more nitrogen, at least 95-100% more nitrogen, or even greaterthan 100% more nitrogen, or even greater than 200% more nitrogen, oreven greater than 300% more nitrogen, or even greater than 400% morenitrogen, or even greater than 500% more nitrogen, when compared withcrop plants grown under normal conditions during an average growingseason.

In another embodiment, the endophyte-associated plant is harvested froma environment where soil contains lower total phosphorus than theoptimum levels recommended in order to achieve average crop yields for aplant grown under average cultivation practices on normal agriculturalland, for example 2-5% less phosphorus than average, for example, atleast 5-10% less phosphorus, at least 10-15% less phosphorus, at least15-20% less phosphorus, at least 20-25% less phosphorus, at least 25-30%less phosphorus, at least 30-35% less phosphorus, at least 35-40% lessphosphorus, at least 40-45% less phosphorus, at least 45-50% lessphosphorus, at least 50-55% less phosphorus, at least 55-60% lessphosphorus, at least 60-65% less phosphorus, at least 65-70% lessphosphorus, at least 70-75% less phosphorus, at least 80-85% lessphosphorus, at least 85-90% less phosphorus, at least 90-95% lessphosphorus, or less, when compared with crop plants grown under normalconditions during an average growing season.

In another embodiment, the endophyte-associated plant is harvested froma environment where soil contains higher total phosphorus than theoptimum levels recommended in order to achieve average crop yields for aplant grown under average cultivation practices on normal agriculturalland, for example 2-5% more phosphorus than average, for example, atleast 5-10% more phosphorus, at least 10-15% more phosphorus, at least15-20% more phosphorus, at least 20-25% more phosphorus, at least 25-30%more phosphorus, at least 30-35% more phosphorus, at least 35-40% morephosphorus, at least 40-45% more phosphorus, at least 45-50% morephosphorus, at least 50-55% more phosphorus, at least 55-60% morephosphorus, at least 60-65% more phosphorus, at least 65-70% morephosphorus, at least 70-75% more phosphorus, at least 80-85% morephosphorus, at least 85-90% more phosphorus, at least 90-95% morephosphorus, at least 95-100% more phosphorus, or even greater than 100%more phosphorus, or even greater than 200% more phosphorus, or evengreater than 300% more phosphorus, or even greater than 400% morephosphorus, or even greater than 500% more phosphorus, when comparedwith crop plants grown under normal conditions during an average growingseason.

In another embodiment, the endophyte-associated plant is harvested froma environment where soil contains lower total potassium than the optimumlevels recommended in order to achieve average crop yields for a plantgrown under average cultivation practices on normal agricultural land,for example 2-5% less potassium than average, for example, at least5-10% less potassium, at least 10-15% less potassium, at least 15-20%less potassium, at least 20-25% less potassium, at least 25-30% lesspotassium, at least 30-35% less potassium, at least 35-40% lesspotassium, at least 40-45% less potassium, at least 45-50% lesspotassium, at least 50-55% less potassium, at least 55-60% lesspotassium, at least 60-65% less potassium, at least 65-70% lesspotassium, at least 70-75% less potassium, at least 80-85% lesspotassium, at least 85-90% less potassium, at least 90-95% lesspotassium, or less, when compared with crop plants grown under normalconditions during an average growing season.

In another embodiment, the endophyte-associated plant is harvested froma environment where soil contains higher total potassium than theoptimum levels recommended in order to achieve average crop yields for aplant grown under average cultivation practices on normal agriculturalland, for example 2-5% more potassium than average, for example, atleast 5-10% more potassium, at least 10-15% more potassium, at least15-20% more potassium, at least 20-25% more potassium, at least 25-30%more potassium, at least 30-35% more potassium, at least 35-40% morepotassium, at least 40-45% more potassium, at least 45-50% morepotassium, at least 50-55% more potassium, at least 55-60% morepotassium, at least 60-65% more potassium, at least 65-70% morepotassium, at least 70-75% more potassium, at least 80-85% morepotassium, at least 85-90% more potassium, at least 90-95% morepotassium, at least 95-100% more potassium, or even greater than 100%more potassium, or even greater than 200% more potassium, or evengreater than 300% more potassium, or even greater than 400% morepotassium, or even greater than 500% more potassium, when compared withcrop plants grown under normal conditions during an average growingseason.

In another embodiment, the endophyte-associated plant is harvested froma environment where soil contains lower total sulfur than the optimumlevels recommended in order to achieve average crop yields for a plantgrown under average cultivation practices on normal agricultural land,for example 2-5% less sulfur than average, for example, at least 5-10%less sulfur, at least 10-15% less sulfur, at least 15-20% less sulfur,at least 20-25% less sulfur, at least 25-30% less sulfur, at least30-35% less sulfur, at least 35-40% less sulfur, at least 40-45% lesssulfur, at least 45-50% less sulfur, at least 50-55% less sulfur, atleast 55-60% less sulfur, at least 60-65% less sulfur, at least 65-70%less sulfur, at least 70-75% less sulfur, at least 80-85% less sulfur,at least 85-90% less sulfur, at least 90-95% less sulfur, or less, whencompared with crop plants grown under normal conditions during anaverage growing season.

In another embodiment, the endophyte-associated plant is harvested froma environment where soil contains higher total sulfur than the optimumlevels recommended in order to achieve average crop yields for a plantgrown under average cultivation practices on normal agricultural land,for example 2-5% more sulfur than average, for example, at least 5-10%more sulfur, at least 10-15% more sulfur, at least 15-20% more sulfur,at least 20-25% more sulfur, at least 25-30% more sulfur, at least30-35% more sulfur, at least 35-40% more sulfur, at least 40-45% moresulfur, at least 45-50% more sulfur, at least 50-55% more sulfur, atleast 55-60% more sulfur, at least 60-65% more sulfur, at least 65-70%more sulfur, at least 70-75% more sulfur, at least 80-85% more sulfur,at least 85-90% more sulfur, at least 90-95% more sulfur, at least95-100% more sulfur, or even greater than 100% more sulfur, or evengreater than 200% more sulfur, or even greater than 300% more sulfur, oreven greater than 400% more sulfur, or even greater than 500% moresulfur, when compared with crop plants grown under normal conditionsduring an average growing season.

In another embodiment, the endophyte-associated plant is harvested froma environment where soil contains lower total calcium than the optimumlevels recommended in order to achieve average crop yields for a plantgrown under average cultivation practices on normal agricultural land,for example 2-5% less calcium than average, for example, at least 5-10%less calcium, at least 10-15% less calcium, at least 15-20% lesscalcium, at least 20-25% less calcium, at least 25-30% less calcium, atleast 30-35% less calcium, at least 35-40% less calcium, at least 40-45%less calcium, at least 45-50% less calcium, at least 50-55% lesscalcium, at least 55-60% less calcium, at least 60-65% less calcium, atleast 65-70% less calcium, at least 70-75% less calcium, at least 80-85%less calcium, at least 85-90% less calcium, at least 90-95% lesscalcium, or less, when compared with crop plants grown under normalconditions during an average growing season.

In another embodiment, the endophyte-associated plant is harvested froma environment where soil contains lower total magnesium than the optimumlevels recommended in order to achieve average crop yields for a plantgrown under average cultivation practices on normal agricultural land,for example 2-5% less magnesium than average, for example, at least5-10% less magnesium, at least 10-15% less magnesium, at least 15-20%less magnesium, at least 20-25% less magnesium, at least 25-30% lessmagnesium, at least 30-35% less magnesium, at least 35-40% lessmagnesium, at least 40-45% less magnesium, at least 45-50% lessmagnesium, at least 50-55% less magnesium, at least 55-60% lessmagnesium, at least 60-65% less magnesium, at least 65-70% lessmagnesium, at least 70-75% less magnesium, at least 80-85% lessmagnesium, at least 85-90% less magnesium, at least 90-95% lessmagnesium, or less, when compared with crop plants grown under normalconditions during an average growing season.

In another embodiment, the endophyte-associated plant is harvested froma environment where soil contains higher total sodium chloride (salt)than the optimum levels recommended in order to achieve average cropyields for a plant grown under average cultivation practices on normalagricultural land, for example 2-5% more salt than average, for example,at least 5-10% more salt, at least 10-15% more salt, at least 15-20%more salt, at least 20-25% more salt, at least 25-30% more salt, atleast 30-35% more salt, at least 35-40% more salt, at least 40-45% moresalt, at least 45-50% more salt, at least 50-55% more salt, at least55-60% more salt, at least 60-65% more salt, at least 65-70% more salt,at least 70-75% more salt, at least 80-85% more salt, at least 85-90%more salt, at least 90-95% more salt, at least 95-100% more salt, oreven greater than 100% more salt, or even greater than 200% more salt,or even greater than 300% more salt, or even greater than 400% moresalt, or even greater than 500% more salt, when compared with cropplants grown under normal conditions during an average growing season.

Relocalization of Endophytes

In some embodiments, a single endophyte strain or a plurality ofendophytes that are used to treat a plant element are capable oflocalizing to a different tissue of the plant, regardless of theoriginal source of the endophyte. For example, the endophyte can becapable of localizing to any one of the tissues in the plant, including:the root, adventitious root, seminal root, root hair, shoot, leaf,flower, bud, tassel, meristem, pollen, pistil, ovaries, stamen, fruit,stolon, rhizome, nodule, tuber, trichome, guard cells, hydathode, petal,sepal, glume, rachis, vascular cambium, phloem, and xylem. In oneembodiment, the endophyte is capable of localizing to the root and/orthe root hair of the plant. In another embodiment, the endophyte iscapable of localizing to the photosynthetic tissues, for example, leavesand shoots of the plant. In other cases, the endophyte is localized tothe vascular tissues of the plant, for example, in the xylem and phloem.In still another embodiment, the endophyte is capable of localizing tothe reproductive tissues (flower, pollen, pistil, ovaries, stamen,fruit) of the plant. In another embodiment, the endophyte is capable oflocalizing to the root, shoots, leaves and reproductive tissues of theplant. In still another embodiment, the endophyte colonizes a fruit orseed tissue of the plant. In still another embodiment, the endophyte isable to colonize the plant such that it is present in the surface of theplant (i.e., its presence is detectably present on the plant exterior,or the episphere of the plant). In still other embodiments, theendophyte is capable of localizing to substantially all, or all, tissuesof the plant. In certain embodiments, the endophyte is not localized tothe root of a plant. In other cases, the endophyte is not localized tothe photosynthetic tissues of the plant.

Endophytes Capable of Altering the Metabolome, Epigenome, orTranscriptome of Plants

The endophytes useful for the invention can also be classified accordingto the changes conferred upon the plant. For example, the endophyte canalter the hormone status or levels of hormone production in the plant,which in turn can affect many physiological parameters, includingflowering time, water efficiency, apical dominance and/or lateral shootbranching, increase in root hair, and alteration in fruit ripening. Theendophyte may also introduce other changes to the plant, includingbiochemical, metabolomic, proteomic, genomic, epigenomic and/ortranscriptomic profiles of endophyte-associated plants can be comparedwith reference agricultural plants under the same conditions.

Metabolomic differences between the plants can be detected using methodsknown in the art. For example, a biological sample (whole tissue,exudate, phloem sap, xylem sap, root exudate, etc.) from theendophyte-associated and reference agricultural plants can be analyzedessentially as described in Fiehn et al., (2000) Nature Biotechnol., 18,1157-1161, or Roessner et al., (2001) Plant Cell, 13, 11-29. Suchmetabolomic methods can be used to detect differences in levels inhormone, nutrients, secondary metabolites, root exudates, phloem sapcontent, xylem sap content, heavy metal content, and the like. Suchmethods are also useful for detecting alterations in microbial contentand status; for example, the presence and levels of bacterial/fungalsignaling molecules (e.g., autoinducers and pheromones), which canindicate the status of group-based behavior of endophytes based on, forexample, population of endophyte-associated and reference agriculturalplants can also be performed to detect changes in expression of at leastone transcript, or a set or network of genes upon endophyte association.Similarly, epigenetic changes can be detected using methylated DNAimmunoprecipitation followed by high-throughput sequencing.

Combinations of Endophytes

Combinations of endophytes can be selected by any one or more of severalcriteria. In one embodiment, compatible endophytes are selected. As usedherein, “compatibility” refers to endophyte populations that do notsignificantly interfere with the growth, propagation, and/or productionof beneficial substances of the other. Incompatible endophytepopulations can arise, for example, where one of the populationsproduces or secrets a compound that is toxic or deleterious to thegrowth of the other population(s). Incompatibility arising fromproduction of deleterious compounds/agents can be detected using methodsknown in the art, and as described herein elsewhere. Similarly, thedistinct populations can compete for limited resources in a way thatmakes co-existence difficult.

In another embodiment, combinations are selected on the basis ofcompounds produced by each population of endophytes. For example, thefirst population is capable of producing siderophores, and anotherpopulation is capable of producing anti-fungal compounds. In anembodiment, the first population of endophytes or endophytic componentsis capable of a function selected from the group consisting of auxinproduction, nitrogen fixation, and production of an antimicrobialcompound, siderophore production, mineral phosphate solubilization,cellulase production, chitinase production, xylanase production, andacetoin production, carbon source utilization, and combinations thereof.In another embodiment, the second population of endophytes or endophyticcomponent is capable of a function selected from the group consisting ofauxin production, nitrogen fixation, production of an antimicrobialcompound, siderophore production, mineral phosphate solubilization,cellulase production, chitinase production, xylanase production, andacetoin production, and combinations thereof. In still anotherembodiment, the first and second populations are capable of at least onedifferent function.

In still another embodiment, the combinations of endophytes are selectedfor their distinct localization in the plant after colonization. Forexample, the first population of endophytes or endophytic components cancolonize, and in some cases preferentially colonize, the root tissue,while a second population can be selected on the basis of itspreferential colonization of the aerial parts of the agricultural plant.Therefore, in an embodiment, the first population is capable ofcolonizing one or more of the tissues selected from the group consistingof a root, shoot, leaf, flower, and seed. In another embodiment, thesecond population is capable of colonizing one or more tissues selectedfrom the group consisting of root, shoot, leaf, flower, and seed. Instill another embodiment, the first and second populations are capableof colonizing a different tissue within the agricultural plant.

In some embodiments, combinations of endophytes are selected for theirability to confer a benefit to the host plant at different points in thelife cycle of said host plant. In one example, one endophyte can beselected to impart improved seedling vigor, and a second endophyte canbe selected to improve soil nutrient acquisition by roots of the matureplant.

In still another embodiment, combinations of endophytes are selected fortheir ability to confer one or more distinct fitness traits on theinoculated agricultural plant, either individually or in synergisticassociation with other endophytes. In another embodiment, one endophytemay induce the colonization of a second endophyte. Alternatively, two ormore endophytes may induce the colonization of a third endophyte. Forexample, the first population of endophytes or endophytic components isselected on the basis that it confers significant increase in biomass,while the second population promotes increased drought tolerance on theinoculated agricultural plant. Therefore, in one embodiment, the firstpopulation is capable of conferring at least one trait selected from thegroup consisting of thermal tolerance, herbicide tolerance, droughtresistance, insect resistance, fungus resistance, virus resistance,bacteria resistance, male sterility, cold tolerance, salt tolerance,increased yield, enhanced nutrient use efficiency, increased nitrogenuse efficiency, increased fermentable carbohydrate content, reducedlignin content, increased antioxidant content, enhanced water useefficiency, increased vigor, increased germination efficiency, earlieror increased flowering, increased biomass, altered root-to-shoot biomassratio, enhanced soil water retention, or a combination thereof. Inanother embodiment, the second population is capable of conferring atrait selected from the group consisting of thermal tolerance, herbicidetolerance, drought resistance, insect resistance, fungus resistance,virus resistance, bacteria resistance, male sterility, cold tolerance,salt tolerance, increased yield, enhanced nutrient use efficiency,increased nitrogen use efficiency, increased fermentable carbohydratecontent, reduced lignin content, increased antioxidant content, enhancedwater use efficiency, increased vigor, increased germination efficiency,earlier or increased flowering, increased biomass, altered root-to-shootbiomass ratio, and enhanced soil water retention. In still anotherembodiment, each of the first and second population is capable ofconferring a different trait selected from the group consisting ofthermal tolerance, herbicide tolerance, drought resistance, insectresistance, fungus resistance, virus resistance, bacteria resistance,male sterility, cold tolerance, salt tolerance, increased yield,enhanced nutrient use efficiency, increased nitrogen use efficiency,increased fermentable carbohydrate content, reduced lignin content,increased antioxidant content, enhanced water use efficiency, increasedvigor, increased germination efficiency, earlier or increased flowering,increased biomass, altered root-to-shoot biomass ratio, and enhancedsoil water retention.

The combinations of endophytes can also be selected based oncombinations of the above criteria. For example, the first population ofendophytes can be selected on the basis of the compound it produces(e.g., its ability to fix nitrogen, thus providing a potential nitrogensource to the plant), while the second population can be selected on thebasis of its ability to confer increased resistance of the plant to apathogen (e.g., a fungal pathogen).

In some embodiments of the present invention, it is contemplated thatcombinations of endophytes can provide an increased benefit to the hostplant, as compared to that conferred by a single endophyte, by virtue ofadditive effects. For example, one endophyte strain that induces abenefit in the host plant may induce such benefit equally well in aplant that is also colonized with a different endophyte strain that alsoinduces the same benefit in the host plant. The host plant thus exhibitsthe same total benefit from the combination of different endophytestrains as the additive benefit to individual plants colonized with eachindividual endophyte of the combination. In one example, a plant iscolonized with two different endophyte strains: one provides a 1×increase in biomass when associated with the plant, and the otherprovides a 2× increase in biomass when associated with a differentplant. When both endophyte strains are associated with the same plant,that plant would experience a 3× (additive of 1×+2× single effects)increase in auxin biomass. Additive effects are a surprising embodimentof the present invention, as non-compatibility of endophytes may resultin a cancelation of the beneficial effects of both endophytes.

In some embodiments of the present invention, it is contemplated that acombination of endophytes can provide an increased benefit to the hostplant, as compared to that conferred by a single endophyte, by virtue ofsynergistic effects. For example, one endophyte strain that induces abenefit in the host plant may induce such benefit beyond additiveeffects in a plant that is also colonized with a different endophytestrain that also induces that benefit in the host plant. The host plantthus exhibits the greater total benefit from the combination ofdifferent endophyte strains than could be seen from the additive benefitof individual plants colonized with each individual endophyte of thecombination. In one example, a plant is colonized with two differentendophyte strains: one provides a 1x increase in biomass when associatedwith a plant, and the other provides a 2× increase in biomass whenassociated with a different plant. When both endophyte strains areassociated with the same plant, that plant would experience a 5×(greater than an additive of 1×+2× single effects) increase in biomass.Synergistic effects are a surprising embodiment of the presentinvention.

Inoculation with Multiple Endophytes

In another embodiment, the present invention contemplates methods ofcoating a plant element, e.g., a seed of a plant, with a plurality ofendophytes, as well as synthetic compositions comprising a plurality ofendophytes on and/or in the plant element. The methods according to thisembodiment can be performed in a manner similar to those describedherein for single endophyte coating. In one example, multiple endophytescan be prepared in a single preparation that is coated onto the plantelement, e.g., a seed. The endophytes can be from a common origin (i.e.,a same plant). Alternatively, the endophytes can be from differentplants.

Where multiple endophytes are coated onto a plant element, eachendophyte can be a bacterium. In the alternative, each endophyte can bea fungus. In still another embodiment, a plurality of bacterial andfungal endophytes can be coated onto the surface of a plant element.

Where a plurality of endophytes are coated onto the plant element, anyor all of the endophytes may be capable of conferring a beneficial traitonto the host plant. In some cases, all of the endophytes are capable ofconferring a beneficial trait onto the host plant. The trait conferredby each of the endophytes may be the same (e.g., both improve the hostplant's tolerance to a particular biotic stress), or may be distinct(e.g., one improves the host plant's tolerance to drought, while anotherimproves phosphate utilization). In other cases the conferred trait maybe the result of interactions between the endophytes.

In one embodiment, an agricultural plant is contacted with a formulationcomprising at least two endophytic microbial entities. Specific examplesof pairs of endophytic microbial entities that can be applied to anagricultural plant include, for example, a pair of endophytic microbescontaining nucleic acid sequences that are each at least 97% identicalto the nucleic acid sequence selected from the groups provided in Table1, Table 2, Table 7 and Table 8.

Isolation of Endophytes

According to the present invention, endophytes are isolated from a plantelement, e.g., a seed of a plant. Because endophytes are capable ofliving and/or residing within the plant, or portion of the plant(including the seed), the endophytic nature of a microbe candistinguished from surface associated microbes by its resistance tosurface sterilization techniques. Therefore, in one embodiment,endophytes are isolated from plant elements after the surface of theplant element is sterilized by contacting with non-specificantimicrobial agents such as sodium hypochlorite, hydrogen peroxide,copper oxychloride, copper hydroxide, copper sulfate, chlorothalonil,cuprous oxide, streptomycin, copper ammonium carbonate, copper diammoniadiacetate complex, copper octanoate, oxytetracycline, fosetyl-AL orchloropicrin, in an aqueous solution and also optionally includingdetergents such as SDS, triton X-100, tween 20, can be used. Inaddition, dried seeds can be soaked in organic solvents such as ethanol,for example 50%-90% ethanol. Antibacterial or antifungal agents (e.g.,captan, maneb, thiram, fludioxonil, etc.), particularly those that donot penetrate into the plant element, can also be used. In general,plant elements are soaked in an aqueous solution or commercialformulation containing one or more of these compounds for 30 seconds to12 hours in a plastic container. After surface sterilization, the plantelement is removed from the antibacterial formulation and washed 3-5times with sterile distilled water. In an alternative embodiment wherethe plant element is a seed, the seed coat can be removed under sterileconditions, and the microbes inside the seed isolated and characterized.

Once surface-residing microbes are removed, the surviving microbespresent in the plant element are generally considered endophytes. Suchendophytes can be a bacterium or fungus, and can be isolated byhomogenizing the surface sterilized seeds, and placing the homogenateunder conditions allowing growth of the microbe. Therefore, the loss ofmicrobe viability upon surface sterilization indicates that the microbesare almost exclusively located on the seed surface. In contrast,resistance of the microbe population to such plant element sterilizationmethods indicates an internal localization of the microbes.Alternatively, the presence of microbial DNA after surface sterilizationwith agents that cross-link or otherwise destroy DNA can be detectedusing sensitive detection methods such as PCR to establish the presenceof the microbe within the plant element.

Growth of Endophytes

Viability of the microbe can be tested after plant element surfacesterilization, or after removal of the seed coat, by homogenizing theplant element and placing the homogenate under conditions that promotegrowth of the microbe. In the alternative, the presence of microbes canbe detected visually or microscopically if the microbes can form acolony that is visible by such inspection. Reagents are also availablefor the detection of microbes: the stain aniline blue can be used fordetecting hyphae, other assays are known in the art.

Endophytes may require special conditions to allow for growth inisolation. A number of different growth media can be used to grow theendophytes. Additional details of endophyte growth are described withinthe examples sections.

Functional Attributes of Endophytes

In some cases, a single endophyte strain, a plurality of endophytes, oreach individual type of endophytes of that plurality, may produce one ormore compounds and/or have one or more activities, e.g., one or more ofthe following: production of a metabolite, production of a phytohormonesuch as auxin, production of acetoin, production of an antimicrobialcompound, production of a siderophore, production of a cellulase,production of a pectinase, production of a chitinase, production of axylanase, nitrogen fixation, or mineral phosphate solubilization. Forexample, an endophyte can produce a phytohormone selected from the groupconsisting of an auxin, a cytokinin, a gibberellin, ethylene, abrassinosteroid, and abscisic acid. In some embodiments, the endophyteproduces auxin (e.g., indole-3-acetic acid (IAA)). Production of auxincan be assayed as described herein. Many of the microbes describedherein are capable of producing the plant hormone auxin indole-3-aceticacid (IAA) when grown in culture. Auxin plays a key role in altering thephysiology of the plant, including the extent of root growth. Therefore,in other embodiments, endophytes are disposed on the surface or within atissue of the plant element in an amount effective to detectablyincrease production of auxin in the agricultural plant when comparedwith a reference agricultural plant. In some embodiments, the increasedauxin production can be detected in a tissue type selected from thegroup consisting of the root, shoot, leaves, and flowers.

In some embodiments, a single endophyte strain, a plurality ofendophytes, or each individual type of endophytes of that plurality, canproduce a compound with antimicrobial properties. For example, thecompound can have antibacterial properties, as determined by the growthassays provided herein. In some embodiments, the compound withantibacterial properties shows bacteriostatic or bactericidal activityagainst E. coli and/or Bacillus sp. In other embodiments, the endophyteproduces a compound with antifungal properties, for example, fungicidalor fungistatic activity against S. cerevisiae and/or Rhizoctonia.

In some embodiments, a single endophyte strain, a plurality ofendophytes, or each individual type of endophytes of that plurality, iscapable of nitrogen fixation, and is thus capable of producing ammoniumfrom atmospheric nitrogen. The ability of endophytes to fix nitrogen canbe confirmed by testing for growth of the fungus in nitrogen-free growthmedia, for example, LGI media, as described herein.

In some embodiments, a single endophyte strain, a plurality ofendophytes, or each individual type of endophytes of that plurality, canproduce a compound that increases the solubility of mineral phosphate inthe medium, i.e., mineral phosphate solubilization, for example, usinggrowth assays known in the art. In some embodiments, the endophytesproduce a compound that allows the bacterium to grow in growth mediacomprising Ca₃HPO₄ as the sole phosphate source.

In some embodiments, a single endophyte strain, a plurality ofendophytes, or each individual type of endophytes of that plurality, canproduce a siderophore. Siderophores are small high-affinity ironchelating agents secreted by microorganisms that increase thebioavailability of iron. Siderophore production by the endophytes can bedetected, for example, using methods known in the art.

In some embodiments, a single endophyte strain, a plurality ofendophytes, or each individual type of endophytes of that plurality, canproduce a hydrolytic enzyme. For example, in some embodiments, anendophytes can produce a hydrolytic enzyme selected from the groupconsisting of a cellulase, a pectinase, a chitinase and a xylanase.Hydrolytic enzymes can be detected using the methods known in the art.

Selection of Endophytes Conferring Beneficial Traits

The present invention contemplates inoculation of plants with microbes.As described earlier, the microbes can be derived from many differentplants species, from different parts of the plants, and from plantsisolated across different environments. Once a microbe is isolated, itcan be tested for its ability to confer a beneficial trait. Numeroustests can be performed both in vitro and in vivo to assess whatbenefits, if any, are conferred upon the plant. In one embodiment, amicrobe is tested in vitro for an activity selected from the groupconsisting of: liberation of complexed phosphates, liberation ofcomplexed iron (e.g., through secretion of siderophores), production ofphytohormones, production of antibacterial compounds, production ofantifungal compounds, production of insecticidal compounds, productionof nematicidal compounds, production and/or secretion of ACC deaminase,production and/or secretion of acetoin, production and/or secretion ofpectinase, production and/or secretion of cellulase, and productionand/or secretion of RNAse. Exemplary in vitro methods for the above canbe found in the Examples sections below.

It is noted that the initial test for the activities listed above canalso be performed using a mixture of microbes, for example, a communityof microbes isolated from a single plant. A positive activity readoutusing such mixture can be followed with the isolation of individualmicrobes within that population and repeating the in vitro tests for theactivities to isolate the microbe responsible for the particularactivity. Once validated using a single microbe isolate, then the plantcan be inoculated with a microbe, and the test performed in vivo, eitherin growth chamber or greenhouse conditions, and comparing with a controlplant that was not inoculated with the microbe.

Endophyte Preparations

Also described herein is a preparation comprising one or more isolatedmodified endophytes described above. The preparation further comprisesan agriculturally acceptable carrier, and the preparation comprises anamount of endophytes sufficient to improve an agronomic trait of thepopulation of seeds. In one embodiment, the isolated endophyte iscultured, for example, on semi-synthetic or synthetic growth medium. Inone embodiment, the endophyte is provided as a powder, for example, alyophilized powder. In another embodiment, the endophyte is applied insuspension at a suitable concentration. The preparation of microbes canbe an aqueous solution, an oil-in-water emulsion or water-in-oilemulsion containing a minimum concentration of a microbe. Microbes arepresent as live cells, viable cells, spores, or mycelia. Typically, theconcentration is at least 10⁴ CFU/ml or spores/ml, for example at least3×10⁴ CFU/mL or spores/ml, at least 10⁵ CFU/mL or spores/ml, at least3×10⁵ CFU/mL or spores/ml, at least 10⁶ CFU/mL or spores/ml, at least3×10⁶ CFU/mL or spores/ml, at least 10⁷ CFU/ml or spores/ml, at least3×10⁷ CFU/mL or spores/ml, at least 10⁸ CFU/mL or spores/ml, 10⁹ CFU/mLor spores/ml, or more. In one embodiment, the preparation is a solutioncontaining a microbe at a concentration between about 10⁵ CFU/mL orspores/ml and about 10⁹ CFU/mL or spores/ml. In another embodiment, thepreparation contains a microbe at a concentration between about 10⁶CFU/mL or spores/ml and about 10⁸ CFU/mL or spores/ml.

The synthetic preparation can also contain any number of othercomponents. In one embodiment, the synthetic preparation may containgrowth media or constituents required for the growth and propagation ofthe microbe. In one embodiment, the growth medium is selected from thegroup provided in the table below.

TABLE 100 Exemplary growth medium Microbe Type Media Organisms BacteriaNutrient Peptone Agar Heterotrophic bacteria MacConkey Agar + myo-Klebsiella Sp. inositol + Carbenicillin J agar Bacillus sp. and otherfirmicutes N-poor Medium (LGT) Aerobic heterotrophic N2-fixing bacteriaYeast Mannitol Agar Rhizobium sp. King's B medium Pseudomonas sp. SCmedium Fastidious bacteria R2A agar Oligotrophic bacteria Tryptic SoyAgar Heterotrophic bacteria Fungi Cornmeal agar Fungi Glucose-Yeastextract Selective enumeration agar + tetracycline of yeasts and molds.Potato-Dextrose agar (PDA) Yeasts and molds Potato-Dextrose broth (PDB)Yeast and molds Sabouraud Agar Yeasts, molds and aciduric microorganismsV8 Agar Fungi Malt Dextrose Agar Identification of yeasts and mouldsCzapek's medium Fungi and Mold SPT agar Verticillium sp.

The synthetic preparation can be of a defined pH range. In oneembodiment, the pH of the preparation can be between pH 5.5-6.0, pH5.75-6.25, pH 6.0-6.5, pH 6.25-6.75, pH 6.5-7.0, pH 6.75-7.25, and pH7.0-7.5. The pH of the medium can be adjusted using any biologicallycompatible buffering agent.

The synthetic preparation can also comprise a carrier, such asdiatomaceous earth, clay, or chitin, which act to complex with chemicalagents, such as control agents.

The synthetic preparation can also comprise an adherent. Such agents areuseful for combining the microbes of the invention with carriers thatcan contain other compounds (e.g., control agents that are notbiologic), to yield a coating composition. Such compositions help createcoatings around the plant or seed to maintain contact between themicrobe and other agents with the plant or plant part. In oneembodiment, adherents are selected from the group consisting of:alginate, gums, starches, lecithins, formononetin, polyvinyl alcohol,alkali formononetinate, hesperetin, polyvinyl acetate, cephalins, GumArabic, Xanthan Gum, Mineral Oil, Polyethylene Glycol (PEG), Polyvinylpyrrolidone (PVP), Arabino-galactan, Methyl Cellulose, PEG 400,Chitosan, Polyacrylamide, Polyacrylate, Polyacrylonitrile, Glycerol,Triethylene glycol, Vinyl Acetate, Gellan Gum, Polystyrene, Polyvinyl,Carboxymethyl cellulose, Gum Ghatti, and polyoxyethylene-polyoxybutyleneblock copolymers. Other examples of adherent compositions that can beused in the synthetic preparation include those described in EP 0818135,CA 1229497, WO 2013090628, EP 0192342, WO 2008103422 and CA 1041788,each of which is incorporated by reference in its entirety.

The synthetic preparation can also contain one or more reagents thatpromote internalization of the microbe into the plant, and can includeany one of the following classes of compounds: a surfactant, anabrasive, an osmoticum, and a plant signaling molecule.

The preparation can also contain a surfactant. Non-limiting examples ofsurfactants include nitrogen-surfactant blends such as Prefer 28(Cenex), Surf-N(US), Inhance (Brandt), P-28 (Wilfarm) and Patrol(Helena); esterified seed oils include Sun-It II (AmCy), MSO (UAP),Scoil (Agsco), Hasten (Wilfarm) and Mes-100 (Drexel); andorgano-silicone surfactants include Silwet L77 (UAP), Silikin (Terra),Dyne-Amic (Helena), Kinetic (Helena), Sylgard 309 (Wilbur-Ellis) andCentury (Precision). In one embodiment, the surfactant is present at aconcentration of between 0.01% v/v to 10% v/v. In another embodiment,the surfactant is present at a concentration of between 0.1% v/v to 1%v/v.

The synthetic preparation of a defined osmolality can also be used. Inone embodiment, the synthetic preparation has an osmolality of less thanabout 100 mOsm, for example less than about 75 mOsm, less than about 50mOsm, or less than about 25 mOsm. In another embodiment, the syntheticpreparation has an osmolality of at least 250 mOsm, for example at least300 mOsm, at least 400 mOsm, at least 500 mOsm, at least 600 mOsm, atleast 700 mOsm, at least 800 mOsm, 900 mOsm or greater. The osmolalityof the preparation can be adjusted by addition of an osmoticum: theosmoticum can be any commonly used osmoticum, and can selected from thegroup consisting of: mannitol, sorbitol, NaCl, KCl, CaCl₂, MgSO₄,sucrose, or any combination thereof.

The endophyte can be obtained from growth in culture, for example, usingsemi-synthetic or synthetic growth medium. In addition, the microbe canbe cultured on solid media, for example on petri dishes, scraped off andsuspended into the preparation. Microbes at different growth phases canbe used. For example, microbes at lag phase, early-log phase, mid-logphase, late-log phase, stationary phase, early death phase, or deathphase can be used.

For certain microbes that exist as mycelia or mycelia-like structures,pre-treatment of the microbes with enzymes (including, but not limitedto, driselase, gluculase, cellulase, beta-glucanase, lysozyme,zymolyase) can be used to generate protoplasts in order to provide asuspension of microbes. After generation of protoplasts, the microbescan be allowed to partially regenerate the cell walls by leaving theprotoplasts in a growth medium or solution with relatively highosmolarity for a short time (typically less than about 12 hours at roomtemperature) to prevent bursting of protoplasts.

Detection and Quantitation of Endophytes and Other Microbes

The presence of the endophyte or other microbes can be detected and itslocalization in or on the host plant (including the seed) can bedetermined using a number of different methodologies. The presence ofthe microbe in the embryo or endosperm, as well as its localization withrespect to the plant cells, can be determined using methods known in theart, including immunofluorescence microscopy using microbe specificantibodies, or fluorescence in situ hybridization. The presence andquantity of other microbes can be established by the FISH,immunofluorescence and PCR methods using probes that are specific forthe microbe. Alternatively, degenerate probes recognizing conservedsequences from many bacteria and/or fungi can be employed to amplify aregion, after which the identity of the microbes present in the testedtissue/cell can be determined by sequencing.

Therefore, in one embodiment, where the endophyte is coated onto thesurface of a plant element of a first plant such that the endophyte ispresent at a higher level on the surface of the plant element than ispresent on the surface of an uncoated reference plant element, the levelof the endophyte present on the surface of the uncoated reference plantelement is determined by culturing microbes that are present on thesurface of the plant element. In another embodiment, the level of theendophyte present on the surface of the uncoated reference plant elementis determined by PCR.

Uniformity of Seeds and Plants

In another aspect, the seeds according to the present invention providea substantially uniform population of seeds with a uniform endophytecomposition. The uniform population of seeds can be of a predefinedweight. For example, a substantially uniform population of seedscontaining at least 100 g seeds, for example at least 1 kg seeds, atleast 5 kg seeds, at least 10 kg seeds, can be provided by the methodaccording to the present invention that contains—as a whole product—morethan 1%, for example more than 5%, more than 10%, more than 20%, morethan 30%, more than 40%, especially more than 50%, of the endophyticmicroorganism, i.e., the strain that is coated onto the surface of theseeds. According to a preferred embodiment, the present inventionprovides a marketable seed product containing at least 100 g seeds, forexample, at least 1 kg seeds, for example at least 5 kg seeds, at least10 kg seeds, wherein—as a whole product-more than 50%, for example, morethan 60%, more than 70%, more than 80%, more than 90%, more than 95%,more than 99%, or 100% of the seeds contain the microbe, i.e., theinoculant strain. Each of the seeds can also contain a uniform number ofmicrobes (for example, viable endophytes): for example, at least 50% ofthe seeds, for example at least 60%, at least 70%, at least 80%, atleast 90%, at least 95%, at least 99%, or more of the seeds in thepopulation can contain at least 100 CFU or spores, at least 300 CFU orspores, at least 1,000 CFU or spores, at least 3,000 CFU or spores, atleast 10,000 CFU or spores, at least 30,000 CFU or spores or more, ofthe endophytic microorganism. In some embodiments, at least 50% of theseeds, for example at least 60%, at least 70%, at least 80%, at least90%, at least 95%, at least 99%, or more of the seeds in the populationcontains a single endophyte or a plurality of endophytes at aconcentration between about 100 CFU or spores and about 30,000 CFU orspores, between about 100 CFU or spores and about 300 CFU or spores,between about 100 CFU or spores and about 1,000 CFU or spores, betweenabout 100 CFU or spores and about 3,000 CFU or spores, between about 100CFU or spores and about 10,00 CFU or spores, between about 100 CFU orspores and about 30,000 CFU or spores, between about 300 CFU or sporesand about 1,000 CFU or spores, between about 300 CFU or spores and about3,000 CFU or spores, between about 300 CFU or spores and about 10,00 CFUor spores, between about 300 CFU or spores and about 30,000 CFU orspores, between about 1,000 CFU or spores and about 3,000 CFU or spores,between about 1,000 CFU or spores and about 10,00 CFU or spores, betweenabout 1,000 CFU or spores and about 30,00 CFU or spores, between about3,000 CFU or spores and about 10,000 CFU or spores, between about 3,000CFU or spores and about 30,00 CFU or spores, or between about 10,000 CFUor spores and about 30,000 CFU or spores. The endophyte can also bequantitated using other means, for example, using quantitative PCR, todetect the total number of endophyte present on each seed.

The uniformity of the microbes within the seed population can bemeasured in several different ways. In one embodiment, a substantialportion of the population of seeds, for example at least 10%, at least20%, at least 30%, at least 40%, at least 50%, at least 60%, at least70%, at least 75%, at least 80%, at least 90%, at least 95% or more ofthe seeds in a population, contains a viable endophyte on its surface.In another embodiment, a substantial portion of the population of seeds,for example at least 10%, at least 20%, at least 30%, at least 40%, atleast 50%, at least 60%, at least 70%, at least 75%, at least 80%, atleast 90%, at least 95% or more of the seeds in a population contain onits surface a threshold number of viable microbe that is at least 1 CFUor spore per seed, at least 10 CFU or spores per seed, for example, atleast 100 CFU or spores, at least 300 CFU or spores, at least 1,000 CFUor spores, at least 3,000 CFU or spores, or more, of the microbe perseed. In some embodiments, a substantial portion of the population ofseeds, for example at least 10%, at least 20%, at least 30%, at least40%, at least 50%, at least 60%, at least 70%, at least 75%, at least80%, at least 90%, at least 95% or more of the seeds in a populationcontain on its surface a threshold number of viable microbe that isbetween 1 CFU or spore per seed and about 3,000 CFU or spores per seed,between 1 CFU or spore per seed and about 10 CFU or spores per seed,between 1 CFU or spore per seed and about 100 CFU or spores per seed,between 1 CFU or spore per seed and about 300 CFU or spores per seed,between 1 CFU or spore per seed and about 1,000 CFU or spores per seed,between 1 CFU or spore per seed and about 3,000 CFU or spores per seed,between about 10 CFU or spore per seed and about 100 CFU or spores perseed, between about 10 CFU or spore per seed and about 300 CFU or sporesper seed, between about 10 CFU or spore per seed and about 1,000 CFU orspores per seed, between about 10 CFU or spore per seed and about 3,000CFU or spores per seed, between about 100 CFU or spore per seed andabout 300 CFU or spores per seed, between about 100 CFU or spore perseed and about 1,000 CFU or spores per seed, between about 100 CFU orspore per seed and about 3,000 CFU or spores per seed, between about 300CFU or spore per seed and about 1,000 CFU or spores per seed, betweenabout 300 CFU or spore per seed and about 3,000 CFU or spores per seed,or between about 1,000 CFU or spore per seed and about 3,000 CFU orspores per seed.

In still another aspect, the present invention discloses a substantiallyuniform population of plants produced by growing the population of seedsdescribed above. In one embodiment, at least 75%, at least 80%, at least90%, at least 95% or more of the plants comprise in one or more tissuesan effective amount of the endophyte or endophytes. In anotherembodiment, at least 1%, between 1% and 10%, for example, at least 10%,between 10% and 20%, at least 20%, between 20% and 30%, at least 30%,between 30% and 40%, at least 40%, between 40% and 50%, at least 50%,between 50% and 60%, at least 60%, between 60% and 70%, at least 70%,between 70% and 75%, at least 75%, between 75% and 80%, at least 80%,between 80% and 90%, at least 90%, between 90% and 95%, at least 95% ormore of the plants comprise a microbe population that is substantiallysimilar.

In some cases, a substantial portion of the population of plants orseeds, for example, at least 1%, between 1% and 10%, for example, atleast 10%, between 10% and 20%, at least 20%, between 20% and 30%, atleast 30%, between 30% and 40%, at least 40%, between 40% and 50%, atleast 50%, between 50% and 60%, at least 60%, between 60% and 70%, atleast 70%, between 70% and 75%, at least 75%, between 75% and 80%, atleast 80%, between 80% and 90%, at least 90%, between 90% and 95%, atleast 95% or more of the seeds in a population, is coated with anendophyte that is able to perform one of the following functions,including: to stimulate plant growth, grow on nitrogen-free media,solubilize phosphate, sequester iron, secrete RNAse, antagonizepathogens, catabolize the precursor of ethylene, produce auxin andacetoin/butanediol. In some cases, a substantial portion of thepopulation of seeds, for example, at least 1%, between 1% and 10%, forexample, at least 10%, between 10% and 20%, at least 20%, between 20%and 30%, at least 30%, between 30% and 40%, at least 40%, between 40%and 50%, at least 50%, between 50% and 60%, at least 60%, between 60%and 70%, at least 70%, between 70% and 75%, at least 75%, between 75%and 80%, at least 80%, between 80% and 90%, at least 90%, between 90%and 95%, at least 95% or more of the seeds in a population, exhibits atleast one of the endophyte community attributes listed in herein (e.g.,total CFUs, presence of a taxa, absence of a taxa, spatial distribution,intercellular colonization, functional properties of endophytes,presence of monoclonal strain, presence of conserved subset of microbialplasmid repertoire, microbe isolated from habitat that is distinct fromthe location of seed production, etc.).

Increased uniformity of microbes in plants or seeds can also be detectedby measuring the presence of non-genomic nucleic acids present in themicrobes. For examples, where the microbe that is inoculated into theplant is known to harbor a plasmid or episome, the presence of theplasmid or episome can be detected in individual plants or seeds byusing conventional methods of nucleic acid detection. Therefore, in oneembodiment, a substantial portion of the population of seeds, forexample at least example at least 1%, between 1% and 10%, for example,at least 10%, between 10% and 20%, at least 20%, between 20% and 30%, atleast 30%, between 30% and 40%, at least 40%, between 40% and 50%, atleast 50%, between 50% and 60%, at least 60%, between 60% and 70%, atleast 70%, between 70% and 75%, at least 75%, between 75% and 80%, atleast 80%, between 80% and 90%, at least 90%, between 90% and 95%, atleast 95% or more of the seeds in a population, has a detectablepresence of the microbial plasmid or episome.

Increased uniformity of the microbes' epigenetic status can also be usedto detect increased uniformity of a population of seeds or plantsderived from such seeds. For example, where a microbe that has beeninoculated by a plant is also present in the plant (for example, in adifferent tissue or portion of the plant), or where the introducedmicrobe is sufficiently similar to a microbe that is present in some ofthe plants (or portion of the plant, including seeds), it is stillpossible to distinguish between the inoculated microbe and the nativemicrobe, for example, by distinguishing between the two microbe types onthe basis of their epigenetic status. Therefore, in one embodiment, theepigenetic status is detected in microbes across individual seeds or theplants that grow from such seeds.

It is also known that certain viruses are associated with endophyticfungi (such as the Curvularia thermal tolerance virus (CThTV) describedin Marquez, L. M., et al., (2007). Science 315: 513-515). Therefore, thepresence and quantity of a virus can be used to measure uniformity ofseeds or plants containing the endophyte. For example, where theinoculated microbe is known to be associated with a virus, the presenceof that virus can be used as a surrogate indicator of uniformity.Therefore, in one embodiment, a substantial portion of the seeds, forexample at least 1%, between 1% and 10%, for example, at least 10%,between 10% and 20%, at least 20%, between 20% and 30%, at least 30%,between 30% and 40%, at least 40%, between 40% and 50%, at least 50%,between 50% and 60%, at least 60%, between 60% and 70%, at least 70%,between 70% and 75%, at least 75%, between 75% and 80%, at least 80%,between 80% and 90%, at least 90%, between 90% and 95%, at least 95% ormore of the seeds, contain the virus. In other embodiments, where one ormore of the endogenous microbes contain associated viruses which are notfound in, and not compatible with the inoculated microbe, the loss(i.e., absence) of the virus can be used to measure uniformity of theseed population. As such, in another embodiment, a substantial portionof the seeds, for example at least 1%, between 1% and 10%, for example,at least 10%, between 10% and 20%, at least 20%, between 20% and 30%, atleast 30%, between 30% and 40%, at least 40%, between 40% and 50%, atleast 50%, between 50% and 60%, at least 60%, between 60% and 70%, atleast 70%, between 70% and 75%, at least 75%, between 75% and 80%, atleast 80%, between 80% and 90%, at least 90%, between 90% and 95%, atleast 95% or more of the seeds, do not contain the virus. In othercases, the genetic sequence of the virus can be used to measure thegenetic similarity of the virus within a population. In one embodiment,a substantial proportion of the seeds, for example, at least 10%, forexample at least 20%, at least 30%, at least 40%, at least 50%, at least60%, at least 70%, at least 80%, at least 90%, at least 95% or more ofthe seeds contain the same virus, for example, as determined by sequenceanalysis.

Such uniformity in microbial composition is unique and is extremelyadvantageous for high-tech and/or industrial agriculture. It allowssignificant standardization with respect to qualitative endophyte loadof seed products. Suitable volumes or weights are those that arecurrently used for plant seeds (e.g., the at least 100 g, at least 1, 5or 10 kg; but also 25 or more, 40 or more, 50 kg or more, even 100 kg ormore, 500 kg or more, 1 ton or more, etc.). Suitable containers orpackages are those traditionally used in plant seed commercialization:however, also other containers with more sophisticated storagecapabilities (e.g., with microbiologically tight wrappings or with gas-or water-proof containments) can be used. The amount of endophytes(qualitatively and quantitatively) contained in the seeds or in themarketable seed product as a whole can be determined by standardtechniques in microbiology readily available to any person skilled inthe art of plant endophyte analysis.

In some cases, a sub-population of agricultural seeds can be furtherselected on the basis of increased uniformity, for example, on the basisof uniformity of microbial population. For example, individual seeds ofpools collected from individual cobs, individual plants, individualplots (representing plants inoculated on the same day) or individualfields can be tested for uniformity of microbial density, and only thosepools meeting specifications (e.g., at least 80% of tested seeds haveminimum density, as determined by quantitative methods describedelsewhere) are combined to provide the agricultural seed sub-population.

The methods described herein can also comprise a validating step. Thevalidating step can entail, for example, growing some seeds collectedfrom the inoculated plants into mature agricultural plants, and testingthose individual plants for uniformity. Such validating step can beperformed on individual seeds collected from cobs, individual plants,individual plots (representing plants inoculated on the same day) orindividual fields, and tested as described above to identify poolsmeeting the required specifications.

Agricultural Field

In another aspect, described herein is an agricultural field, includinga greenhouse, comprising the population of plants described above. Inone embodiment, the agricultural field comprises at least 100 plants. Inanother embodiment, the population occupies at least about 100 squarefeet of space, wherein at least about 10%, 20%, 30%, 40%, 50%, 60%, 70%,80%, 90% or more than 90% of the population comprises an effectiveamount of the microbe. In another embodiment, the population occupies atleast about 100 square feet of space, wherein at least 1%, between 1%and 10%, for example, at least 10%, between 10% and 20%, at least 20%,between 20% and 30%, at least 30%, between 30% and 40%, at least 40%,between 40% and 50%, at least 50%, between 50% and 60%, at least 60%,between 60% and 70%, at least 70%, between 70% and 75%, at least 75%,between 75% and 80%, at least 80%, between 80% and 90%, at least 90%,between 90% and 95%, at least 95% or more of the population comprisesthe microbe in reproductive tissue. In still another embodiment, thepopulation occupies at least about 100 square feet of space, wherein atleast about 10%, 20%, 30%, 40%, 50%, 60%, 70%, 80%, 90% or more than 90%of the population comprises at least 10 CFUs or spores, 100 CFUs orspores, 1,000 CFUs or spores, 10,000 CFUs or spores or more of themicrobe. In still another embodiment, the population occupies at leastabout 100 square feet of space, wherein at least 1%, between 1% and 10%,for example, at least 10%, between 10% and 20%, at least 20%, between20% and 30%, at least 30%, between 30% and 40%, at least 40%, between40% and 50%, at least 50%, between 50% and 60%, at least 60%, between60% and 70%, at least 70%, between 70% and 75%, at least 75%, between75% and 80%, at least 80%, between 80% and 90%, at least 90%, between90% and 95%, at least 95% or more of the population comprises betweenabout 10 CFU or spores and about 10,000 CFU or spores, between about 10CFU or spores and about 100 CFU or spores, between about 10 CFU orspores and about 1,000 CFU or spores, between about 100 CFU or sporesand about 1,000 CFU or spores, between about 100 CFU or spores and about10,00 CFU or spores, or between about 1,000 CFU or spores and about10,000 CFU or spores. In yet another embodiment, the population occupiesat least about 100 square feet of space, wherein at least 1%, between 1%and 10%, for example, at least 10%, between 10% and 20%, at least 20%,between 20% and 30%, at least 30%, between 30% and 40%, at least 40%,between 40% and 50%, at least 50%, between 50% and 60%, at least 60%,between 60% and 70%, at least 70%, between 70% and 75%, at least 75%,between 75% and 80%, at least 80%, between 80% and 90%, at least 90%,between 90% and 95%, at least 95% or more of the population comprises aexogenous microbe (i.e., the endophyte) of monoclonal origin.

Plants can be grown individually from the seeds coated with theendophytes to propagate the desired microbes in indoor or outdoorsettings. An advantage of the present invention is that it allowsmultiple plants harboring endophytes to be grown under agriculturalmethods as a means of providing improved uniformity of microbe-derivedbenefits to farmers.

Therefore, in another aspect, provided herein are indoor arrangements ofpopulations (e.g., greenhouse) of plants generated from the methods ofthe present invention. Such arrangements can include at least a definednumber of plants of the present invention, such as at least 1, at least2, at least 3, between 3 and 5, at least 5, between 5 and 10, at least10, between 10 and 15, at least 15, between 15 and 20, at least 20,between 20 and 30, at least 30, between 30 and 50, at least 50, between50 and 100, at least 100, between 100 and 200, at least 200, between 200and 500, at least 500, between 500 and 1000, at least 1000, between 1000and 5000, at least 5000, between 5000 and 10000, at least 10000 or moreplants.

Also provided herein are agricultural fields that contain population ofplants generated from the seeds of the present invention. Agriculturalfields can occupy as little as 100 square feet or less, or can occupyhundreds or thousands of acres. Area of field containing a population ofmicrobe-associated plants can be measured in square feet, such as atleast 100, 500, 1000, 5000, 10,000, 50,000 or greater than 50,000 squarefeet, or can be measured in acres, such as least 1, at least 2, at least3, between 3 and 5, at least 5, between 5 and 10, at least 10, between10 and 15, at least 15, between 15 and 20, at least 20, between 20 and30, at least 30, between 30 and 50, at least 50, between 50 and 100, atleast 100, between 100 and 200, at least 200, between 200 and 500, atleast 500, between 500 and 1000, at least 1000, between 1000 and 5000,at least 5000, between 5000 and 10000, at least 10000, between 10000 and50000, at least 50000 or greater acres. The field can also be measuredin hectares, for example at least 1, at least 2, at least 3, between 3and 5, at least 5, between 5 and 10, at least 10, between 10 and 15, atleast 15, between 15 and 20, at least 20, between 20 and 30, at least30, between 30 and 50, at least 50, between 50 and 100, at least 100,between 100 and 200, at least 200, between 200 and 500, at least 500,between 500 and 1000, at least 1000, between 1000 and 5000, at least5000, between 5000 and 10000, at least 10000 or more hectares.Additionally, a field containing a population of microbe-associatedplants can be characterized by the number of plants in the population,generally a field is at least two, such as at least 3, between 3 and 5,at least 5, between 5 and 10, at least 10, between 10 and 15, at least15, between 15 and 20, at least 20, between 20 and 30, at least 30,between 30 and 50, at least 50, between 50 and 100, at least 100,between 100 and 200, at least 200, between 200 and 500, at least 500,between 500 and 1000, at least 1000, between 1000 and 5000, at least5000, between 5000 and 10000, at least 10000, between 10000 and 25000,at least 250000, between 25000 and 50000, at least 500000, between 50000and 75000, at least 750000, between 75000 and 100000, at least 1000000or more plants. A field is generally a contiguous area but may beseparated by geographical features such as roads, waterways, buildings,fences, and the like known to those skilled in the art. Because themicrobe-associated plants described herein benefit from an increasedlevel of uniformity of germination and other characteristics, it isdesirable to maximize the percentage of plants containing microbes. Forexample, at least 10% (e.g., between 10% and 20%, at least 20%, between20% and 30%, at least 30%, between 30% and 40%, at least 40%, between40% and 50%, at least 50%, between 50% and 60%, at least 60%, between60% and 70%, at least 70%, between 70% and 75%, at least 75%, between75% and 80%, at least 80%, between 80% and 90%, at least 90%, between90% and 95%, between 95% and 99%, at least 99% or more) of the plantscontain the microbes.

Endophytes Compatible with Agrichemicals

In certain embodiments, the endophyte is selected on the basis of itscompatibility with commonly used agrichemicals. As mentioned earlier,plants, particularly agricultural plants, can be treated with a vastarray of agrichemicals, including fungicides, biocides (anti-bacterialagents), herbicides, insecticides, nematicides, rodenticides,fertilizers, and other agents.

In some cases, it can be important for the endophyte to be compatiblewith agrichemicals, particularly those with fungicidal or antibacterialproperties, in order to persist in the plant although, as mentionedearlier, there are many such fungicidal or antibacterial agents that donot penetrate the plant, at least at a concentration sufficient tointerfere with the endophyte. Therefore, where a systemic fungicide orantibacterial agent is used in the plant, compatibility of the endophyteto be inoculated with such agents will be an important criterion.

In one embodiment, natural isolates of endophytes that are compatiblewith agrichemicals can be used to inoculate the plants according to themethods described herein. For example, fungal endophytes which arecompatible with agriculturally employed fungicides can be isolated byplating a culture of the endophytes on a petri dish containing aneffective concentration of the fungicide, and isolating colonies of theendophyte that are compatible with the fungicide. In another embodiment,an endophyte that is compatible with a fungicide is used for the methodsdescribed herein. Fungicide compatible endophytes can also be isolatedby selection on liquid medium. The culture of endophytes can be platedon petri dishes without any forms of mutagenesis; alternatively, theendophytes can be mutagenized using any means known in the art. Forexample, microbial cultures can be exposed to UV light,gamma-irradiation, or chemical mutagens such as ethylmethanesulfonate(EMS) prior to selection on fungicide containing media. Finally, wherethe mechanism of action of a particular fungicide is known, the targetgene can be specifically mutated (either by gene deletion, genereplacement, site-directed mutagenesis, etc.) to generate an endophytethat is resilient against that particular fungicide. It is noted thatthe above-described methods can be used to isolate fungi that arecompatible with both fungistatic and fungicidal compounds.

It will also be appreciated by one skilled in the art that a plant maybe exposed to multiple types of fungicides or antibacterial compounds,either simultaneously or in succession, for example at different stagesof plant growth. Where the target plant is likely to be exposed tomultiple fungicidal and/or antibacterial agents, an endophyte that iscompatible with many or all of these agrichemicals can be used toinoculate the plant. An endophyte that is compatible with severalfungicidal agents can be isolated, for example, by serial selection. Anendophyte that is compatible with the first fungicidal agent is isolatedas described above (with or without prior mutagenesis). A culture of theresulting endophyte can then be selected for the ability to grow onliquid or solid media containing the second antifungal compound (again,with or without prior mutagenesis). Colonies isolated from the secondselection are then tested to confirm its compatibility to bothantifungal compounds.

Likewise, bacterial endophytes that are compatible to biocides(including herbicides such as glyphosate or antibacterial compounds,whether bacteriostatic or bactericidal) that are agriculturally employedcan be isolated using methods similar to those described for isolatingfungicide compatible endophytes. In one embodiment, mutagenesis of themicrobial population can be performed prior to selection with anantibacterial agent. In another embodiment, selection is performed onthe microbial population without prior mutagenesis. In still anotherembodiment, serial selection is performed on an endophyte: the endophyteis first selected for compatibility to a first antibacterial agent. Theisolated compatible endophyte is then cultured and selected forcompatibility to the second antibacterial agent. Any colony thusisolated is tested for compatibility to each, or both antibacterialagents to confirm compatibility with these two agents.

Resistance, or compatibility with an antimicrobial agent can bedetermined by a number of means known in the art, including thecomparison of the minimal inhibitory concentration (MIC) of theunmodified and modified endophyte. Therefore, in one embodiment, thepresent invention discloses an isolated modified endophyte derived froman endophyte isolated from within a plant or tissue thereof, wherein theendophyte is modified such that it exhibits at least 3 fold greater, forexample, at least 5 fold greater, at least 10 fold greater, at least 20fold greater, at least 30 fold greater or more MIC to an antimicrobialagent when compared with the unmodified endophyte.

In one particular aspect, disclosed herein are bacterial endophytes withenhanced resistance to the herbicide glyphosate. In one embodiment, thebacterial endophyte has a doubling time in growth medium containing atleast 1 mM glyphosate, for example, at least 2 mM glyphosate, at least 5mM glyphosate, at least 10 mM glyphosate, at least 15 mM glyphosate ormore, that is no more than 250%, for example, no more than 200%, no morethan 175%, no more than 150%, or no more than 125%, of the doubling timeof the endophyte in the same growth medium containing no glyphosate. Inone particular embodiment, the bacterial endophyte has a doubling timein growth medium containing 5 mM glyphosate that is no more than 150%the doubling time of the endophyte in the same growth medium containingno glyphosate.

In another embodiment, the bacterial endophyte has a doubling time in aplant tissue containing at least 10 ppm glyphosate, for example, atleast 15 ppm glyphosate, at least 20 ppm glyphosate, at least 30 ppmglyphosate, at least 40 ppm glyphosate or more, that is no more than250%, for example, no more than 200%, no more than 175%, no more than150%, or no more than 125%, of the doubling time of the endophyte in areference plant tissue containing no glyphosate. In one particularembodiment, the bacterial endophyte has a doubling time in a planttissue containing 40 ppm glyphosate that is no more than 150% thedoubling time of the endophyte in a reference plant tissue containing noglyphosate.

The selection process described above can be repeated to identifyisolates of the endophyte that are compatible with a multitude ofantifungal or antibacterial agents.

Candidate isolates can be tested to ensure that the selection foragrichemical compatibility did not result in loss of a desired microbialbioactivity. Isolates of the endophyte that are compatible with commonlyemployed fungicides can be selected as described above. The resultingcompatible endophyte can be compared with the parental endophyte onplants in its ability to promote germination.

The agrichemical compatible endophytes generated as described above canbe detected in samples. For example, where a transgene was introduced torender the endophyte resistant to the agrichemical(s), the transgene canbe used as a target gene for amplification and detection by PCR. Inaddition, where point mutations or deletions to a portion of a specificgene or a number of genes results in compatibility with theagrichemical(s), the unique point mutations can likewise be detected byPCR or other means known in the art. Such methods allow the detection ofthe microbe even if it is no longer viable. Thus, commodity plantproducts produced using the agrichemical compatible microbes describedherein can readily be identified by employing these and related methodsof nucleic acid detection.

Improved Traits Conferred by the Endophyte

The present invention contemplates the establishment of a microbialsymbiont in a plant. In one embodiment, the microbial associationresults in a detectable change to the seed or plant. The detectablechange can be an improvement in a number of agronomic traits (e.g.,improved general health, increased response to biotic or abioticstresses, or enhanced properties of the plant or a plant part, includingfruits and grains). Alternatively, the detectable change can be aphysiological or biological change that can be measured by methods knownin the art. The detectable changes are described in more detail in thesections below. As used herein, an endophyte is considered to haveconferred an improved agricultural trait whether or not the improvedtrait arose from the plant, the endophyte, or the concerted actionbetween the plant and endophyte. Therefore, for example, whether abeneficial hormone or chemical is produced by the plant or endophyte,for purposes of the present invention, the endophyte will be consideredto have conferred an improved agronomic trait upon the host plant.

In some embodiments, plant-endophyte combinations confer an agronomicbenefit in agricultural plants. In some embodiments, the agronomic traitis selected from the group consisting of altered oil content, alteredprotein content, altered seed carbohydrate composition, altered seed oilcomposition, and altered seed protein composition, chemical tolerance,cold tolerance, delayed senescence, disease resistance, droughttolerance, ear weight, growth improvement, health enhancement, heattolerance, herbicide tolerance, herbivore resistance, improved nitrogenfixation, improved nitrogen utilization, improved root architecture,improved water use efficiency, increased biomass, increased root length,increased seed weight, increased shoot length, increased yield,increased yield under water-limited conditions, kernel mass, kernelmoisture content, metal tolerance, number of ears, number of kernels perear, number of pods, nutrition enhancement, pathogen resistance, pestresistance, photosynthetic capability improvement, salinity tolerance,stay-green, vigor improvement, increased dry weight of mature seeds,increased fresh weight of mature seeds, increased number of mature seedsper plant, increased chlorophyll content, increased number of pods perplant, increased length of pods per plant, reduced number of wiltedleaves per plant, reduced number of severely wilted leaves per plant,and increased number of non-wilted leaves per plant, a detectablemodulation in the level of a metabolite, a detectable modulation in thelevel of a transcript, and a detectable modulation in the proteomerelative to a reference plant. In other embodiments, at least twoagronomic traits are improved in the agricultural plant.

For example, the endophyte may provide an improved benefit or toleranceto a plant that is of at least 3%, between 3% and 5%, at least 5%,between 5% and 10%, least 10%, between 10% and 15%, for example at least15%, between 15% and 20%, at least 20%, between 20% and 30%, at least30%, between 30% and 40%, at least 40%, between 40% and 50%, at least50%, between 50% and 60%, at least 60%, between 60% and 75%, at least75%, between 75% and 100%, at least 100%, between 100% and 150%, atleast 150%, between 150% and 200%, at least 200%, between 200% and 300%,or at least 300% or more, when compared with uninoculated plants grownunder the same conditions.

In some aspects, provided herein, are methods for producing a seed of aplant with a heritably altered trait. The trait of the plant can bealtered without known genetic modification of the plant genome, andcomprises the following steps. First, a preparation of an isolatedendophyte that is exogenous to the seed of the plant is provided, andoptionally processed to produce a microbial preparation. The microbialpreparation is then contacted with the plant. The plants are thenallowed to go to seed, and the seeds, which contain the endophytes onand/or in the seed are collected. The endophytes contained within theseed are viably incorporated into the seed.

The method of the present invention can facilitate crop productivity byenhancing germination, seedling vigor and biomass in comparison with anon-treated control. Moreover, the introduction of the beneficialmicroorganisms to within the seed instead of by, e.g., seed coating,makes the endophytes less susceptible to environmental perturbation andmore compatible with chemical seed coatings (e.g., pesticides andherbicides). Using endophyte colonized seeds, the plant growth andbiomass increases are statistically similar to those obtained usingconventional inoculation methods e.g., exogenous seed soaking and soilinoculation (that are more laborious and less practicable in certaincircumstances).

Improved General Health

Also described herein are plants, and fields of plants, that areassociated with beneficial endophytes, such that the overall fitness,productivity or health of the plant or a portion thereof, is maintained,increased and/or improved over a period of time. Improvement in overallplant health can be assessed using numerous physiological parametersincluding, but not limited to, height, overall biomass, root and/orshoot biomass, seed germination, seedling survival, photosyntheticefficiency, transpiration rate, seed/fruit number or mass, plant grainor fruit yield, leaf chlorophyll content, photosynthetic rate, rootlength, or any combination thereof. Improved plant health, or improvedfield health, can also be demonstrated through improved resistance orresponse to a given stress, either biotic or abiotic stress, or acombination of one or more abiotic stresses, as provided herein.

Other Abiotic Stresses

Disclosed herein are endophyte-associated plants with increasedresistance to an abiotic stress. Exemplary abiotic stresses include, butare not limited to: drought, salt, high metal content, low nutrients,cold stress, and heat stress.

Drought and Heat Tolerance

When soil water is depleted or if water is not available during periodsof drought, crop yields are restricted. Plant water deficit develops iftranspiration from leaves exceeds the supply of water from the roots.The available water supply is related to the amount of water held in thesoil and the ability of the plant to reach that water with its rootsystem. Transpiration of water from leaves is linked to the fixation ofcarbon dioxide by photosynthesis through the stomata. The two processesare positively correlated so that high carbon dioxide influx throughphotosynthesis is closely linked to water loss by transpiration. Aswater transpires from the leaf, leaf water potential is reduced and thestomata tend to close in a hydraulic process limiting the amount ofphotosynthesis. Since crop yield is dependent on the fixation of carbondioxide in photosynthesis, water uptake and transpiration arecontributing factors to crop yield. Plants which are able to use lesswater to fix the same amount of carbon dioxide or which are able tofunction normally at a lower water potential have the potential toconduct more photosynthesis and thereby to produce more biomass andeconomic yield in many agricultural systems.

In some cases, a plant resulting from seeds or other plant elementstreated with a single endophyte strain or a plurality of endophytes canexhibit a physiological change, such as a compensation of thestress-induced reduction in photosynthetic activity (expressed, forexample, as ΔFv/Fm) after exposure to heat shock or drought conditionsas compared to a corresponding control, genetically identical plant thatdoes not contain the endophytes grown in the same conditions. In somecases, the endophyte-associated plant as disclosed herein can exhibit anincreased change in photosynthetic activity ΔFv(ΔFv/Fm) after heat-shockor drought stress treatment, for example 1, 2, 3, 4, 5, 6, 7 days ormore after the heat-shock or drought stress treatment, or untilphotosynthesis ceases, as compared with corresponding control plant ofsimilar developmental stage but not comprising the endophytes. Forexample, a plant having a plurality of the endophytes able to conferheat and/or drought-tolerance can exhibit a ΔFv/Fm of from about 0.1 toabout 0.8 after exposure to heat-shock or drought stress or a ΔFv/Fmrange of from about 0.03 to about 0.8 under one day, or 1, 2, 3, 4, 5,6, 7, or over 7 days post heat-shock or drought stress treatment, oruntil photosynthesis ceases. In some embodiments, stress-inducedreductions in photosynthetic activity can be compensated by at leastabout 0.25% (for example, at least about 0.5%, between 0.5% and 1%, atleast about 1%, between 1% and 2%, at least about 2%, between 2% and 3%,at least about 3%, between 3% and 5%, at least about 5%, between 5% and10%, at least about 8%, at least about 10%, between 10% and 15%, atleast about 15%, between 15% and 20%, at least about 20%, between 20$and 25%, at least about 25%, between 25% and 30%, at least about 30%,between 30% and 40%, at least about 40%, between 40% and 50%, at leastabout 50%, between 50% and 60%, at least about 60%, between 60% and 75%,at least about 75%, between 75% and 80%, at least about 80%, between 80%and 85%, at least about 85%, between 85% and 90%, at least about 90%,between 90% and 95%, at least about 95%, between 95% and 99%, at leastabout 99%, between 99% and 100%, or at least 100%) as compared to thephotosynthetic activity decrease in a corresponding referenceagricultural plant following heat shock conditions. Significance of thedifference between endophyte-associated and reference agriculturalplants can be established upon demonstrating statistical significance,for example at p<0.05 with an appropriate parametric or non-parametricstatistic, e.g., Chi-square test, Student's t-test, Mann-Whitney test,or F-test based on the assumption or known facts that theendophyte-associated plant and reference agricultural plant haveidentical or near identical genomes (isoline comparison).

In selecting traits for improving crops, a decrease in water use,without a change in growth would have particular merit in an irrigatedagricultural system where the water input costs were high. An increasein growth without a corresponding jump in water use would haveapplicability to all agricultural systems. In many agricultural systemswhere water supply is not limiting, an increase in growth, even if itcame at the expense of an increase in water use also increases yield.Water use efficiency (WUE) is a parameter often correlated with droughttolerance, and is the CO2 assimilation rate per water transpired by theplant. An increased water use efficiency of the plant relates in somecases to an increased fruit/kernel size or number. Therefore, in someembodiments, the plants described herein exhibit an increased water useefficiency when compared with a reference agricultural plant grown underthe same conditions. For example, the plants grown from the plantelements comprising the plurality of endophytes can have at least 3%,between 3% and 5%, at least 5%, between 5% and 10%, least 10%, between10% and 15%, for example at least 15%, between 15% and 20%, at least20%, between 20% and 30%, at least 30%, between 30% and 40%, at least40%, between 40% and 50%, at least 50%, between 50% and 60%, at least60%, between 60% and 75%, at least 75%, between 75% and 100%, or atleast 100% higher WUE than a reference agricultural plant grown underthe same conditions. Such an increase in WUE can occur under conditionswithout water deficit, or under conditions of water deficit, forexample, when the soil water content is less than or equal to 60% ofwater saturated soil, for example, less than or equal to 50%, less thanor equal to 40%, less than or equal to 30%, less than or equal to 20%,less than or equal to 10% of water saturated soil on a weight basis. Ina related embodiment, the plant comprising the plurality of endophytescan have at least 10% higher relative water content (RWC), for example,at least 3%, between 3% and 5%, at least 5%, between 5% and 10%, least10%, between 10% and 15%, for example at least 15%, between 15% and 20%,at least 20%, between 20% and 30%, at least 30%, between 30% and 40%, atleast 40%, between 40% and 50%, at least 50%, between 50% and 60%, atleast 60%, between 60% and 75%, at least 75%, between 75% and 100%, orat least 100% higher RWC than a reference agricultural plant grown underthe same conditions.

In some embodiments, the plants comprise a single endophyte strain or aplurality of endophytes able to increase heat and/or drought-tolerancein sufficient quantity, such that increased growth or improved recoveryfrom wilting under conditions of heat or drought stress is observed. Forexample, a plurality of endophyte populations described herein can bepresent in sufficient quantity in a plant, resulting in increased growthas compared to a plant that does not contain endophytes, when grownunder drought conditions or heat shock conditions, or following suchconditions. Increased heat and/or drought tolerance can be assessed withphysiological parameters including, but not limited to, increasedheight, overall biomass, root and/or shoot biomass, seed germination,seedling survival, photosynthetic efficiency, transpiration rate,seed/fruit number or mass, plant grain or fruit yield, leaf chlorophyllcontent, photosynthetic rate, root length, wilt recovery, turgorpressure, or any combination thereof, as compared to a referenceagricultural plant grown under similar conditions. For example, theendophyte may provide an improved benefit or tolerance to a plant thatis of at least 3%, between 3% and 5%, at least 5%, between 5% and 10%,least 10%, between 10% and 15%, for example at least 15%, between 15%and 20%, at least 20%, between 20% and 30%, at least 30%, between 30%and 40%, at least 40%, between 40% and 50%, at least 50%, between 50%and 60%, at least 60%, between 60% and 75%, at least 75%, between 75%and 100%, or at least 100%, when compared with uninoculated plants grownunder the same conditions.

In various embodiments, a single endophyte strain or plurality ofendophytes introduced into altered seed microbiota can confer in theresulting plant thermal tolerance, herbicide tolerance, droughtresistance, insect resistance, fungus resistance, virus resistance,bacteria resistance, male sterility, cold tolerance, salt tolerance,increased yield, enhanced nutrient use efficiency, increased nitrogenuse efficiency, increased protein content, increased fermentablecarbohydrate content, reduced lignin content, increased antioxidantcontent, enhanced water use efficiency, increased vigor, increasedgermination efficiency, earlier or increased flowering, increasedbiomass, altered root-to-shoot biomass ratio, enhanced soil waterretention, or a combination thereof. A difference between theendophyte-associated plant and a reference agricultural plant can alsobe measured using other methods known in the art.

Salt Stress

In other embodiments, a single endophyte strain or plurality ofendophytes able to confer increased tolerance to salinity stress can beintroduced into plants. The resulting plants comprising endophytes canexhibit increased resistance to salt stress, whether measured in termsof survival under saline conditions, or overall growth during, orfollowing salt stress. The physiological parameters of plant healthrecited above, including height, overall biomass, root and/or shootbiomass, seed germination, seedling survival, photosynthetic efficiency,transpiration rate, seed/fruit number or mass, plant grain or fruityield, leaf chlorophyll content, photosynthetic rate, root length, orany combination thereof, can be used to measure growth, and comparedwith the growth rate of reference agricultural plants (e.g., isogenicplants without the endophytes) grown under identical conditions. Forexample, the endophyte may provide an improved benefit or tolerance to aplant that is of at least 3%, between 3% and 5%, at least 5%, between 5%and 10%, least 10%, between 10% and 15%, for example at least 15%,between 15% and 20%, at least 20%, between 20% and 30%, at least 30%,between 30% and 40%, at least 40%, between 40% and 50%, at least 50%,between 50% and 60%, at least 60%, between 60% and 75%, at least 75%,between 75% and 100%, or at least 100%, when compared with uninoculatedplants grown under the same conditions.

In other instances, endophyte-associated plants and referenceagricultural plants can be grown in soil or growth media containingdifferent concentration of sodium to establish the inhibitoryconcentration of sodium (expressed, for example, as the concentration inwhich growth of the plant is inhibited by 50% when compared with plantsgrown under no sodium stress). Therefore, in another embodiment, a plantresulting from seeds containing an endophyte able to confer salttolerance described herein exhibits an increase in the inhibitory sodiumconcentration by at least 10 mM, for example at least 15 mM, at least 20mM, at least 30 mM, at least 40 mM, at least 50 mM, at least 60 mM, atleast 70 mM, at least 80 mM, at least 90 mM, at least 100 mM or more,when compared with the reference agricultural plants.

High Metal Content

Plants are sessile organisms and therefore must contend with theenvironment in which they are placed. While plants have adapted manymechanisms to deal with chemicals and substances that may be deleteriousto their health, heavy metals represent a class of toxins which arehighly relevant for plant growth and agriculture. Plants use a number ofmechanisms to cope with toxic levels of heavy metals (for example,nickel, cadmium, lead, mercury, arsenic, or aluminum) in the soil,including excretion and internal sequestration. For agriculturalpurposes, it is important to have plants that are able to tolerateotherwise hostile conditions, for example soils containing elevatedlevels of toxic heavy metals. Endophytes that are able to conferincreased heavy metal tolerance may do so by enhancing sequestration ofthe metal in certain compartments. Use of such endophytes in a plantwould allow the development of novel plant-endophyte combinations forpurposes of environmental remediation (also known as phytoremediation).Therefore, in one embodiment, the plant containing the endophyte able toconfer increased metal tolerance exhibits a difference in aphysiological parameter that is at least about 5% greater, for exampleat least about 5%, at least about 8%, at least about 10%, at least about15%, at least about 20%, at least about 25%, at least about 30%, atleast about 40%, at least about 50%, at least about 60%, at least about75%, at least about 80%, at least about 80%, at least about 90%, or atleast 100%, at least about 200%, at least about 300%, at least about400% or greater than a reference agricultural plant grown under the sameheavy metal concentration in the soil.

Alternatively, the inhibitory concentration of the heavy metal can bedetermined for the endophyte-associated plant and compared with areference agricultural plant under the same conditions. Therefore, inone embodiment, the plants resulting from seeds containing an endophyteable to confer heavy metal tolerance described herein exhibit anincrease in the inhibitory sodium concentration by at least 0.1 mM, forexample at least 0.3 mM, at least 0.5 mM, at least 1 mM, at least 2 mM,at least 5 mM, at least 10 mM, at least 15 mM, at least 20 mM, at least30 mM, at least 50 mM or more, when compared with the referenceagricultural plants.

Finally, plants inoculated with endophytes that are able to conferincreased metal tolerance exhibits an increase in overall metalaccumulation by at least 10%, for example at least 15%, at least 20%, atleast 30%, at least 40%, at least 50%, at least 60%, at least 75%, atleast 100%, at least 150%, at least 200%, at least 300% or more, whencompared with uninoculated plants grown under the same conditions.

Low Nutrient Stress

A single endophyte strain or a plurality of endophytes described hereinmay also confer to the plant an increased ability to grow in nutrientlimiting conditions, for example by solubilizing or otherwise makingavailable to the plants macronutrients or micronutrients that arecomplexed, insoluble, or otherwise in an unavailable form. In someembodiments, a plant is inoculated with a plurality of endophytes thatconfer increased ability to liberate and/or otherwise provide to theplant with nutrients selected from the group consisting of phosphate,nitrogen, potassium, iron, manganese, calcium, molybdenum, vitamins, orother micronutrients. Such a plant can exhibit increased growth in soilcomprising limiting amounts of such nutrients when compared withreference agricultural plant. Differences between theendophyte-associated plant and reference agricultural plant can bemeasured by comparing the biomass of the two plant types grown underlimiting conditions, or by measuring the physical parameters describedabove. Therefore, in some embodiments, the plant comprising endophytesshows increased tolerance to nutrient limiting conditions as compared toa reference agricultural plant grown under the same nutrient limitedconcentration in the soil, as measured for example by increased biomassor seed yield of at least 3%, between 3% and 5%, at least 5%, between 5%and 10%, least 10%, between 10% and 15%, for example at least 15%,between 15% and 20%, at least 20%, between 20% and 30%, at least 30%,between 30% and 40%, at least 40%, between 40% and 50%, at least 50%,between 50% and 60%, at least 60%, between 60% and 75%, at least 75%,between 75% and 100%, or at least 100%, when compared with uninoculatedplants grown under the same conditions. In other embodiments, the plantcontaining the plurality of endophytes is able to grown under nutrientstress conditions while exhibiting no difference in the physiologicalparameter compared to a plant that is grown without nutrient stress. Insome embodiments, such a plant will exhibit no difference in thephysiological parameter when grown with 2-5% less nitrogen than averagecultivation practices on normal agricultural land, for example, at least10%, between 10% and 15%, for example at least 15%, between 15% and 20%,at least 20%, between 20% and 30%, at least 30%, between 30% and 40%, atleast 40%, between 40% and 50%, at least 50%, between 50% and 60%, atleast 60%, between 60% and 75%, at least 75%, or between 75% and 100%,less nitrogen, when compared with crop plants grown under normalconditions during an average growing season. In some embodiments, themicrobe capable of providing nitrogen-stress tolerance to a plant isdiazotrophic. In other embodiments, the microbe capable of providingnitrogen-stress tolerance to a plant is non-diazotrophic.

Cold Stress

In some cases, endophytes can confer to the plant the ability totolerate cold stress. Many known methods exist for the measurement of aplant's tolerance to cold stress (as reviewed, for example, in Thomashow(2001) Plant Physiol. 125: 89-93, and Gilmour et al. (2000) PlantPhysiol. 124: 1854-1865, both of which are incorporated herein byreference in their entirety). As used herein, cold stress refers to boththe stress induced by chilling (0° C.-15° C.) and freezing (<0° C.).Some cultivars of agricultural plants can be particularly sensitive tocold stress, but cold tolerance traits may be multigenic, making thebreeding process difficult. Endophytes able to confer cold tolerancewould potentially reduce the damage suffered by farmers on an annualbasis. Improved response to cold stress can be measured by survival ofplants, the amount of necrosis of parts of the plant, or a change incrop yield loss, as well as the physiological parameters used in otherexamples. Therefore, in one embodiment, the plant containing theendophyte able to confer increased cold tolerance exhibits a differencein a physiological parameter that is at least about 5% greater, forexample at least about 5%, at least about 8%, at least about 10%, atleast about 15%, at least about 20%, at least about 25%, at least about30%, at least about 40%, at least about 50%, at least about 60%, atleast about 75%, at least about 80%, at least about 80%, at least about90%, or at least 100%, at least about 200%, at least about 300%, atleast about 400% or greater than a reference agricultural plant grownunder the same conditions of cold stress.

Biotic Stress

In other embodiments, a single endophyte strain or plurality ofendophytes protects the plant from a biotic stress, for example, insectinfestation, nematode infestation, complex infection, fungal infection,oomycete infection, protozoal infection, viral infection, and herbivoregrazing, or a combination thereof. For example, the endophyte mayprovide an improved benefit or tolerance to a plant that is of at least3%, between 3% and 5%, at least 5%, between 5% and 10%, least 10%,between 10% and 15%, for example at least 15%, between 15% and 20%, atleast 20%, between 20% and 30%, at least 30%, between 30% and 40%, atleast 40%, between 40% and 50%, at least 50%, between 50% and 60%, atleast 60%, between 60% and 75%, at least 75%, between 75% and 100%, orat least 100%, when compared with uninoculated plants grown under thesame conditions.

Insect Herbivory

There are an abundance of insect pest species that can infect or infesta wide variety of plants. Pest infestation can lead to significantdamage. Insect pests that infest plant species are particularlyproblematic in agriculture as they can cause serious damage to crops andsignificantly reduce plant yields. A wide variety of different types ofplant are susceptible to pest infestation including commercial cropssuch as cotton, soybean, wheat, barley, and corn.

In some embodiments, endophytes described herein confer upon the hostplant the ability to repel insect herbivores. In other cases, theendophytes may produce, or induce the production in the plant of,compounds which are insecticidal or insect repellant. The insect may beany one of the common pathogenic insects affecting plants, particularlyagricultural plants. Examples include, but are not limited to:Leptinotarsa spp. (e.g., L. decemlineata (Colorado potato beetle), L.juncta (false potato beetle), or L. texana (Texan false potato beetle));Nilaparvata spp. (e.g., N. lugens (brown planthopper)); Laode/phax spp.(e.g., L. striatellus (small brown planthopper)); Nephotettix spp.(e.g., N. virescens or N. cincticeps (green leafhopper), or N.nigropictus (rice leafhopper)); Sogatella spp. (e.g., S. furcifera(white-backed planthopper)); Chilo spp. (e.g., C. suppressalis (ricestriped stem borer), C. auricilius (gold-fringed stem borer), or C.polychrysus (dark-headed stem borer)); Sesamia spp. (e.g., S. inferens(pink rice borer)); Tryporyza spp. (e.g., T. innotata (white riceborer), or T. incertulas (yellow rice borer)); Anthonomus spp. (e.g., A.grandis (boll weevil)); Phaedon spp. (e.g., P. cochleariae (mustard leafbeetle)); Epilachna spp. (e.g., E. varivetis (Mexican bean beetle));Tribolium spp. (e.g., T. castaneum (red floor beetle)); Diabrotica spp.(e.g., D. virgifera (western corn rootworm), D. barberi (northern cornrootworm), D. undecimpunctata howardi (southern corn rootworm), D.virgifera zeae (Mexican corn rootworm); Ostrinia spp. (e.g., O.nubilalis (European corn borer)); Anaphothrips spp. (e.g., A. obscrurus(grass thrips)); Pectinophora spp. (e.g., P. gossypiella (pinkbollworm)); Heliothis spp. (e.g., H. virescens (tobacco budworm));Trialeurodes spp. (e.g., T. abutiloneus (banded-winged whitefly) T.vaporariorum (greenhouse whitefly)); Bemisia spp. (e.g., B. argentifolii(silverleaf whitefly)); Aphis spp. (e.g., A. gossypii (cotton aphid));Lygus spp. (e.g., L. lineolaris (tarnished plant bug) or L. hesperus(western tarnished plant bug)); Euschistus spp. (e.g., E. conspersus(consperse stink bug)); Chlorochroa spp. (e.g., C. sayi (Say stinkbug));Nezara spp. (e.g., N. viridula (southern green stinkbug)); Thrips spp.(e.g., T. tabaci (onion thrips)); Frankliniella spp. (e.g., F. fusca(tobacco thrips), or F. occidentalis (western flower thrips)); Achetaspp. (e.g., A. domesticus (house cricket)); Myzus spp. (e.g., M.persicae (green peach aphid)); Macrosiphum spp. (e.g., M. euphorbiae(potato aphid)); Blissus spp. (e.g., B. leucopterus (chinch bug));Acrosternum spp. (e.g., A. hilare (green stink bug)); Chilotraea spp.(e.g., C. polychrysa (rice stalk borer)); Lissorhoptrus spp. (e.g., L.oryzophilus (rice water weevil)); Rhopalosiphum spp. (e.g., R. maidis(corn leaf aphid)); Anuraphis spp. (e.g., A. maidiradicis (corn rootaphid)), and combinations thereof.

The endophyte-associated plant can be tested for its ability to resist,or otherwise repel, pathogenic insects by measuring, for example, insectload, overall plant biomass, biomass of the fruit or grain, percentageof intact leaves, or other physiological parameters described herein,and comparing with a reference agricultural plant. In some embodiments,the endophyte-associated plant exhibits increased biomass as compared toa reference agricultural plant grown under the same conditions (e.g.,grown side-by-side, or adjacent to, endophyte-associated plants). Inother embodiments, the endophyte-associated plant exhibits increasedfruit or grain yield as compared to a reference agricultural plant grownunder the same conditions (e.g., grown side-by-side, or adjacent to,endophyte-associated plants). In any of the above, the endophyte mayprovide an improved benefit or tolerance to a plant that is of at least3%, between 3% and 5%, at least 5%, between 5% and 10%, least 10%,between 10% and 15%, for example at least 15%, between 15% and 20%, atleast 20%, between 20% and 30%, at least 30%, between 30% and 40%, atleast 40%, between 40% and 50%, at least 50%, between 50% and 60%, atleast 60%, between 60% and 75%, at least 75%, between 75% and 100%, orat least 100%, when compared with uninoculated plants grown under thesame conditions.

Nematodes

Nematodes are microscopic roundworms that feed on the roots, fluids,leaves and stems of more than 2,000 row crops, vegetables, fruits, andornamental plants, causing an estimated $100 billion crop loss worldwideand accounting for 13% of global crop losses due to disease. A varietyof parasitic nematode species infect crop plants, including root-knotnematodes (RKN), cyst- and lesion-forming nematodes. Root-knotnematodes, which are characterized by causing root gall formation atfeeding sites, have a relatively broad host range and are thereforeparasitic on a large number of crop species. The cyst- andlesion-forming nematode species have a more limited host range, butstill cause considerable losses in susceptible crops.

Signs of nematode damage include stunting and yellowing of leaves, andwilting of the plants during hot periods. Nematode infestation, however,can cause significant yield losses without any obvious above-grounddisease symptoms. The primary causes of yield reduction are due tounderground root damage. Roots infected by SCN are dwarfed or stunted.Nematode infestation also can decrease the number of nitrogen-fixingnodules on the roots, and may make the roots more susceptible to attacksby other soil-borne plant nematodes.

In some embodiments, the endophyte-associated plant has an increasedresistance to a nematode when compared with a reference agriculturalplant. As before with insect herbivores, biomass of the plant or aportion of the plant, or any of the other physiological parametersmentioned elsewhere, can be compared with the reference agriculturalplant grown under the same conditions. Particularly useful measurementsinclude overall plant biomass, biomass and/or size of the fruit orgrain, and root biomass. In some embodiments, the endophyte-associatedplant exhibits increased biomass as compared to a reference agriculturalplant grown under the same conditions (e.g., grown side-by-side, oradjacent to, the endophyte-associated plants, under conditions ofnematode challenge). In other embodiments, the endophyte-associatedplant exhibits increased root biomass as compared to a referenceagricultural plant grown under the same conditions (e.g., grownside-by-side, or adjacent to, the endophyte-associated plants, underconditions of nematode challenge). In still another embodiment, theendophyte-associated plant exhibits increased fruit or grain yield ascompared to a reference agricultural plant grown under the sameconditions (e.g., grown side-by-side, or adjacent to, theendophyte-associated plants, under conditions of nematode challenge). Inany of the above, the endophyte may provide an improved benefit ortolerance to a plant that is of at least 3%, between 3% and 5%, at least5%, between 5% and 10%, least 10%, between 10% and 15%, for example atleast 15%, between 15% and 20%, at least 20%, between 20% and 30%, atleast 30%, between 30% and 40%, at least 40%, between 40% and 50%, atleast 50%, between 50% and 60%, at least 60%, between 60% and 75%, atleast 75%, between 75% and 100%, or at least 100%, when compared withuninoculated plants grown under the same conditions.

Fungal Pathogens

Fungal diseases are responsible for yearly losses of over $10 Billion onagricultural crops in the US, represent 42% of global crop losses due todisease, and are caused by a large variety of biologically diversepathogens. Different strategies have traditionally been used to controlthem. Resistance traits have been bred into agriculturally importantvarieties, thus providing various levels of resistance against either anarrow range of pathogen isolates or races, or against a broader range.However, this involves the long and labor intensive process ofintroducing desirable traits into commercial lines by genetic crossesand, due to the risk of pests evolving to overcome natural plantresistance, a constant effort to breed new resistance traits intocommercial lines is required. Alternatively, fungal diseases have beencontrolled by the application of chemical fungicides. This strategyusually results in efficient control, but is also associated with thepossible development of resistant pathogens and can be associated with anegative impact on the environment. Moreover, in certain crops, such asbarley and wheat, the control of fungal pathogens by chemical fungicidesis difficult or impractical.

The present invention contemplates the use a single endophyte strain orof a plurality of endophytes that is able to confer resistance to fungalpathogens to the host plant. Increased resistance to fungal inoculationcan be measured, for example, using any of the physiological parameterspresented above, by comparing with reference agricultural plants. Insome embodiments, the endophyte-associated plant exhibits increasedbiomass and/or less pronounced disease symptoms as compared to areference agricultural plant grown under the same conditions (e.g.,grown side-by-side, or adjacent to, the endophyte-associated plants,infected with the fungal pathogen). In still another embodiment, theendophyte-associated plant exhibits increased fruit or grain yield ascompared to a reference agricultural plant grown under the sameconditions (e.g., grown side-by-side, or adjacent to, theendophyte-associated plants, infected with the fungal pathogen). Inother embodiments, the endophyte-associated plant exhibits decreasedhyphal growth as compared to a reference agricultural plant grown underthe same conditions (e.g., grown side-by-side, or adjacent to, theendophyte-associated plants, infected with the fungal pathogen). In anyof the above, the endophyte may provide an improved benefit or toleranceto a plant that is of at least 3%, between 3% and 5%, at least 5%,between 5% and 10%, least 10%, between 10% and 15%, for example at least15%, between 15% and 20%, at least 20%, between 20% and 30%, at least30%, between 30% and 40%, at least 40%, between 40% and 50%, at least50%, between 50% and 60%, at least 60%, between 60% and 75%, at least75%, between 75% and 100%, or at least 100%, when compared withuninoculated plants grown under the same conditions.

Viral Pathogens

Plant viruses are estimated to account for 18% of global crop losses dueto disease. There are numerous examples of viral pathogens affectingagricultural productivity. Examples include the American wheat striatemosaic virus (AWSMV) (wheat striate mosaic), Barley stripe mosaic virus(BSMV), Barley yellow dwarf virus (BYDV), Brome mosaic virus (BMV),Cereal chlorotic mottle virus (CCMV), Corn chlorotic vein banding virus(CCVBV), Brazilian maize mosaic virus, Corn lethal necrosis Viruscomplex from Maize chlorotic mottle virus, (MCMV), Maize dwarf mosaicvirus (MDMV), A or B Wheat streak mosaic virus (WSMV), Cucumber mosaicvirus (CMV), Cynodon chlorotic streak virus (CCSV), Johnsongrass mosaicvirus (JGMV), Maize bushy stunt Mycoplasma-like organism (MLO)associated virus, Maize chlorotic dwarf Maize chlorotic dwarf virus(MCDV), Maize chlorotic mottle virus (MCMV), Maize dwarf mosaic virus(MDMV), strains A, D, E and F, Maize leaf fleck virus (MLFV), Maize linevirus (MLV), Maize mosaic (corn leaf stripe, Maize mosaic virus (MMV),enanismo rayado), Maize mottle and chlorotic stunt virus, Maize pellucidringspot virus (MPRV), Maize raya gruesa virus (MRGV), Maize rayado fino(fine striping) virus (MRFV), Maize red stripe virus (MRSV), Maize ringmottle virus (MRMV), Maize rio cuarto virus (MRCV), Maize rough dwarfvirus (MRDV), Cereal tillering disease virus, Maize sterile stunt virus,barley yellow striate virus, Maize streak virus (MSV), Maize stripevirus, Maize chloroticstripe virus, maize hoja blanca virus, Maizestunting virus; Maize tassel abortion virus (MTAV), Maize vein enationvirus (MVEV), Maize wallaby ear virus (MWEV), Maize white leaf virus,Maize white line mosaic virus (MWLMV), Millet red leaf virus (MRLV),Northern cereal mosaic virus (NCMV), Oat pseudorosette virus,(zakuklivanie), Oat sterile dwarf virus (OSDV), Rice black-streakeddwarf virus (RBSDV), Rice stripe virus (RSV), Sorghum mosaic virus(SrMV), Sugarcane mosaic virus (SCMV) strains H, 1 and M, Sugarcane Fijidisease virus (FDV), Sugarcane mosaic virus (SCMV) strains A, B, D, E,SC, BC, Sabi and MB (formerly MDMV-B), and Wheat spot mosaic virus(WSMV). In one embodiment, the endophyte-associated plant providesprotection against viral pathogens such that there is at least 5%greater biomass, for example, at least 10%, at least 15%, at least 20%,at least 30%, at least 40%, at least 50%, at least 75%, at least 100% ormore biomass, than the reference agricultural plant grown under the sameconditions. In still another embodiment, the endophyte-associated plantexhibits at least 5% greater fruit or grain yield, for example, at least10%, at least 15%, at least 20%, at least 30%, at least 40%, at least50%, at least 75%, at least 100% or more fruit or grain yield whenchallenged with a virus, as compared to a reference agricultural plantgrown under the same conditions. In yet another embodiment, theendophyte-associated plant exhibits at least 5% lower viral titer, forexample, at least 10%, at least 15%, at least 20%, at least 30%, atleast 40%, at least 50%, at least 75%, at least 100% lower viral titerwhen challenged with a virus, as compared to a reference agriculturalplant grown under the same conditions.

Bacterial Pathogens

Likewise, bacterial pathogens are a significant problem negativelyaffecting agricultural productivity and accounting for 27% of globalcrop losses due to plant disease. In one embodiment, theendophyte-associated plant described herein provides protection againstbacterial pathogens such that there is at least 5% greater biomass, forexample, at least 10%, at least 15%, at least 20%, at least 30%, atleast 40%, at least 50%, at least 75%, at least 100% or more biomass,than the reference agricultural plant grown under the same conditions.In still another embodiment, the endophyte-associated plant exhibits atleast 5% greater fruit or grain yield, for example, at least 10%, atleast 15%, at least 20%, at least 30%, at least 40%, at least 50%, atleast 75%, at least 100% or more fruit or grain yield when challengedwith a bacterial pathogen, than the reference agricultural plant grownunder the same conditions. In yet another embodiment, theendophyte-associated plant exhibits at least 5% lower bacterial count,for example, at least 10%, at least 15%, at least 20%, at least 30%, atleast 40%, at least 50%, at least 75%, at least 100% lower bacterialcount when challenged with a bacteria, as compared to a referenceagricultural plant grown under the same conditions.

Yield and Biomass Improvement

In other embodiments, the improved trait can be an increase in overallbiomass of the plant or a part of the plant, including its fruit orseed. In some embodiments, a single endophyte strain or a plurality ofendophytes is disposed on the surface or within a tissue of the plantelement in an amount effective to increase the biomass of the plant, ora part or tissue of the plant grown from the plant element. Theincreased biomass is useful in the production of commodity productsderived from the plant. Such commodity products include an animal feed,a fish fodder, a cereal product, a processed human-food product, a sugaror an alcohol. Such products may be a fermentation product or afermentable product, one such exemplary product is a biofuel. Theincrease in biomass can occur in a part of the plant (e.g., the roottissue, shoots, leaves, etc.), or can be an increase in overall biomass.Increased biomass production, such an increase meaning at at least 3%,between 3% and 5%, at least 5%, between 5% and 10%, least 10%, between10% and 15%, for example at least 15%, between 15% and 20%, at least20%, between 20% and 30%, at least 30%, between 30% and 40%, at least40%, between 40% and 50%, at least 50%, between 50% and 60%, at least60%, between 60% and 75%, at least 75%, between 75% and 100%, or atleast 100%, when compared with uninoculated plants grown under the sameconditions. Such increase in overall biomass can be under relativelystress-free conditions. In other cases, the increase in biomass can bein plants grown under any number of abiotic or biotic stresses,including drought stress, salt stress, heat stress, cold stress, lownutrient stress, nematode stress, insect herbivory stress, fungalpathogen stress, bacterial pathogen stress, and viral pathogen stress.In some embodiments, a plurality of endophytes is disposed in an amounteffective to increase root biomass by at least 3%, between 3% and 5%, atleast 5%, between 5% and 10%, least 10%, between 10% and 15%, forexample at least 15%, between 15% and 20%, at least 20%, between 20% and30%, at least 30%, between 30% and 40%, at least 40%, between 40% and50%, at least 50%, between 50% and 60%, at least 60%, between 60% and75%, at least 75%, between 75% and 100%, or at least 100%, when comparedwith uninoculated plants grown under the same conditions, when comparedwith a reference agricultural plant.

In other cases, a plurality of endophytes is disposed on the plantelement in an amount effective to increase the average biomass of thefruit or cob from the resulting plant at least 3%, between 3% and 5%, atleast 5%, between 5% and 10%, least 10%, between 10% and 15%, forexample at least 15%, between 15% and 20%, at least 20%, between 20% and30%, at least 30%, between 30% and 40%, at least 40%, between 40% and50%, at least 50%, between 50% and 60%, at least 60%, between 60% and75%, at least 75%, between 75% and 100%, or at least 100%, when comparedwith uninoculated plants grown under the same conditions.

Increase in Plant Growth Hormones

Many of the microbes described herein are capable of producing the planthormone auxin indole-3-acetic acid (IAA) when grown in culture. Auxinmay play a key role in altering the physiology of the plant, includingthe extent of root growth. Therefore, in other embodiments, a singleendophyte strain or a plurality of endophytes is disposed on the surfaceor within a tissue of the plant element in an amount effective todetectably induce production of auxin in the agricultural plant. Forexample, the increase in auxin production can be at least 2%, at least3%, at least 4%, at least 5%, at least 6%, at least 7%, at least 8%, atleast 9%, at least 10%, at least 15%, for example, at least 20%, atleast 30%, at least 40%, at least 50%, at least 60%, at least 75%, atleast 100%, or more, when compared with a reference agricultural plant.In some embodiments, the increased auxin production can be detected in atissue type selected from the group consisting of the root, shoot,leaves, and flowers.

Improvement of other traits. In other embodiments, a single endophytestrain or a plurality of endophytes can confer other beneficial traitsto the plant. Improved traits can include an improved nutritionalcontent of the plant or plant element used for human consumption. Insome embodiments, the endophyte-associated plant is able to produce adetectable change in the content of at least one nutrient. Examples ofsuch nutrients include amino acid, protein, oil (including any one ofOleic acid, Linoleic acid, Alpha-linoleic acid, Saturated fatty acids,Palmitic acid, Stearic acid and Trans fats), carbohydrate (includingsugars such as sucrose, glucose and fructose, starch, or dietary fiber),Vitamin A, Thiamine (vit. B1), Riboflavin (vit. B2), Niacin (vit. B3),Pantothenic acid (B5), Vitamin B6, Folate (vit. B9), Choline, Vitamin C,Vitamin E, Vitamin K, Calcium, Iron, Magnesium, Manganese, Phosphorus,Potassium, Sodium, Zinc. In some embodiments, the endophyte-associatedplant or part thereof contains at least one increased nutrient whencompared with reference agricultural plants.

In other cases, the improved trait can include reduced content of aharmful or undesirable substance when compared with referenceagricultural plants. Such compounds include those which are harmful wheningested in large quantities or are bitter tasting (for example, oxalicacid, amygdalin, certain alkaloids such as solanine, caffeine, nicotine,quinine and morphine, tannins, cyanide). As such, in some embodiments,the endophyte-associated plant or part thereof contains less of theundesirable substance when compared with reference agricultural plant.In a related embodiment, the improved trait can include improved tasteof the plant or a part of the plant, including the fruit or seed. In arelated embodiment, the improved trait can include reduction ofundesirable compounds produced by other endophytes in plants, such asdegradation of Fusarium-produced deoxynivalenol (also known as vomitoxinand a virulence factor involved in Fusarium head blight of maize andwheat) in a part of the plant, including the fruit or seed.

The endophyte-associated plant can also have an altered hormone statusor altered levels of hormone production when compared with a referenceagricultural plant. An alteration in hormonal status may affect manyphysiological parameters, including flowering time, water efficiency,apical dominance and/or lateral shoot branching, increase in root hair,and alteration in fruit ripening.

The association between the endophytes and the plant can also bedetected using other methods known in the art. For example, thebiochemical, genomic, epigenomic, transcriptomic, metabolomics, and/orproteomic profiles of endophyte-associated plants can be compared withreference agricultural plants under the same conditions.

Transcriptome analysis of endophyte-associated and referenceagricultural plants can also be performed to detect changes inexpression of at least one transcript, or a set or network of genes uponendophyte association. Similarly, epigenetic changes can be detectedusing methylated DNA immunoprecipitation followed by high-throughputsequencing.

Metabolomic or proteomic differences between the plants can be detectedusing methods known in the art. The metabolites, proteins, or othercompounds described herein can be detected using any suitable methodincluding, but not limited to gel electrophoresis, liquid and gas phasechromatography, either alone or coupled to mass spectrometry, NMR,immunoassays (enzyme-linked immunosorbent assays (ELISA)), chemicalassays, spectroscopy and the like. In some embodiments, commercialsystems for chromatography and NMR analysis are utilized. Suchmetabolomic methods can be used to detect differences in levels inhormone, nutrients, secondary metabolites, root exudates, phloem sapcontent, xylem sap content, heavy metal content, and the like. Suchmethods are also useful for detecting alterations in endophyte contentand status; for example, the presence and levels of signaling molecules(e.g., autoinducers and pheromones), which can indicate the status ofgroup-based behavior of endophytes based on, for example, populationdensity. In some embodiments, a biological sample (whole tissue,exudate, phloem sap, xylem sap, root exudate, etc.) fromendophyte-associated and reference agricultural plants can be analyzedessentially as known in the art.

In some embodiments, metabolites in plants can be modulated by makingsynthetic combinations of plants with pluralities of endophytes. Forexample, a plurality of endophytes can cause a detectable modulation(e.g., an increase or decrease) in the level of various metabolites,e.g., indole-3-carboxylic acid, trans-zeatin, abscisic acid, phaseicacid, indole-3-acetic acid, indole-3-butyric acid, indole-3-acrylicacid, jasmonic acid, jasmonic acid methyl ester, dihydrophaseic acid,gibberellin A3, salicylic acid, upon colonization of a plant.

In some embodiments, a single endophyte strain or a plurality ofendophytes modulates the level of the metabolite directly (e.g., themicrobes produces the metabolite, resulting in an overall increase inthe level of the metabolite found in the plant). In other cases, theagricultural plant, as a result of the association with the plurality ofendophytes, exhibits a modulated level of the metabolite (e.g., theplant reduces the expression of a biosynthetic enzyme responsible forproduction of the metabolite as a result of the microbe inoculation). Instill other cases, the modulation in the level of the metabolite is aconsequence of the activity of both the microbe and the plant (e.g., theplant produces increased amounts of the metabolite when compared with areference agricultural plant, and the endophyte also produces themetabolite). Therefore, as used herein, a modulation in the level of ametabolite can be an alteration in the metabolite level through theactions of the microbe and/or the inoculated plant.

The levels of a metabolite can be measured in an agricultural plant, andcompared with the levels of the metabolite in a reference agriculturalplant, and grown under the same conditions as the inoculated plant. Theuninoculated plant that is used as a reference agricultural plant is aplant that has not been applied with a formulation with the plurality ofendophytes (e.g., a formulation comprising a plurality of populations ofpurified endophytes). The uninoculated plant used as the referenceagricultural plant is generally the same species and cultivar as, and isisogenic to, the inoculated plant.

The metabolite whose levels are modulated (e.g., increased or decreased)in the endophyte-associated plant may serve as a primary nutrient (i.e.,it provides nutrition for the humans and/or animals who consume theplant, plant tissue, or the commodity plant product derived therefrom,including, but not limited to, a sugar, a starch, a carbohydrate, aprotein, an oil, a fatty acid, or a vitamin). The metabolite can be acompound that is important for plant growth, development or homeostasis(for example, a phytohormone such as an auxin, cytokinin, gibberellin, abrassinosteroid, ethylene, or abscisic acid, a signaling molecule, or anantioxidant). In other embodiments, the metabolite can have otherfunctions. For example, in some embodiments, a metabolite can havebacteriostatic, bactericidal, fungistatic, fungicidal or antiviralproperties. In other embodiments, the metabolite can haveinsect-repelling, insecticidal, nematode-repelling, or nematicidalproperties. In still other embodiments, the metabolite can serve a rolein protecting the plant from stresses, may help improve plant vigor orthe general health of the plant. In yet another embodiment, themetabolite can be a useful compound for industrial production. Forexample, the metabolite may itself be a useful compound that isextracted for industrial use, or serve as an intermediate for thesynthesis of other compounds used in industry. In a particularembodiment, the level of the metabolite is increased within theagricultural plant or a portion thereof such that it is present at aconcentration of at least 0.1 ug/g dry weight, for example, at least 0.3ug/g dry weight, between 0.3 ug/g and 1.0 ug/g dry weight, at least 1.0ug/g dry weight, between 1.0 ug/g and 3.0 ug/g dry weight, at least 3.0ug/g dry weight, between 3.0 ug/g and 10 ug/g dry weight, at least 10ug/g dry weight, between 10 ug/g and 30 ug/g dry weight, at least 30ug/g dry weight, between 30 ug/g and 100 ug/g dry weight, at least 100ug/g dry weight, between 100 ug/g and 300 ug/g dry weight, at least 300ug/g dry weight, between 300 ug/g and 1 mg/g dry weight, or more than 1mg/g dry weight, of the plant or portion thereof.

Likewise, the modulation can be a decrease in the level of a metabolite.The reduction can be in a metabolite affecting the taste of a plant or acommodity plant product derived from a plant (for example, a bittertasting compound), or in a metabolite which makes a plant or theresulting commodity plant product otherwise less valuable (for example,reduction of oxalate content in certain plants, or compounds which aredeleterious to human and/or animal health). The metabolite whose levelis to be reduced can be a compound that affects quality of a commodityplant product (e.g., reduction of lignin levels).

Commodity Plant Product

The present invention provides a commodity plant product, as well asmethods for producing a commodity plant product, that is derived from aplant of the present invention. As used herein, a “commodity plantproduct” refers to any composition or product that is comprised ofmaterial derived from a plant, seed, plant cell, or plant part of thepresent invention. Commodity plant products may be sold to consumers andcan be viable or nonviable. Nonviable commodity products include but arenot limited to nonviable seeds and grains; processed seeds, seed parts,and plant parts; dehydrated plant tissue, frozen plant tissue, andprocessed plant tissue; seeds and plant parts processed for animal feedfor terrestrial and/or aquatic animal consumption, oil, meal, flour,flakes, bran, fiber, paper, tea, coffee, silage, crushed of whole grain,and any other food for human or animal consumption; and biomasses andfuel products; and raw material in industry. Industrial uses of oilsderived from the agricultural plants described herein includeingredients for paints, plastics, fibers, detergents, cosmetics,lubricants, and biodiesel fuel. Soybean oil may be split,inter-esterified, sulfurized, epoxidized, polymerized, ethoxylated, orcleaved. Designing and producing soybean oil derivatives with improvedfunctionality and improved oliochemistry is a rapidly growing field. Thetypical mixture of triglycerides is usually split and separated intopure fatty acids, which are then combined with petroleum-derivedalcohols or acids, nitrogen, sulfonates, chlorine, or with fattyalcohols derived from fats and oils to produce the desired type of oilor fat. Commodity plant products also include industrial compounds, suchas a wide variety of resins used in the formulation of adhesives, films,plastics, paints, coatings and foams.

In some cases, commodity plant products derived from the plants, orusing the methods of the present invention can be identified readily. Insome cases, for example, the presence of viable endophytes can bedetected using the methods described herein elsewhere. In other cases,particularly where there are no viable endophytes, the commodity plantproduct may still contain at least a detectable amount of the specificand unique DNA corresponding to the microbes described herein. Anystandard method of detection for polynucleotide molecules may be used,including methods of detection disclosed herein.

Formulations for Agricultural Use

The present invention contemplates a synthetic combination of a plantelement that is associated with a single endophyte strain or a pluralityof endophytes to confer an improved trait of agronomic importance to thehost plant, or an improved agronomic trait potential to a plant elementassociated with the endophytes, that upon and after germination willconfer said benefit to the resultant host plant.

In some embodiments, the plant element is associated with a singleendophyte strain or a plurality of endophytes on its surface. Suchassociation is contemplated to be via a mechanism selected from thegroup consisting of: spraying, immersion, coating, encapsulating,dusting, dripping, aerosolizing, seed treatment, root wash, seedlingsoak, foliar application, soil inocula, in-furrow application, sidedressapplication, soil pre-treatment, wound inoculation, drip tapeirrigation, vector-mediation via a pollinator, injection, osmopriming,hydroponics, aquaponics, and aeroponics.

In some embodiments, the plant element is a leaf, and the syntheticcombination is formulated for application as a foliar treatment.

In some embodiments, the plant element is a seed, and the syntheticcombination is formulated for application as a seed coating.

In some embodiments, the plant element is a root, and the syntheticcombination is formulated for application as a root treatment.

In certain embodiments, the plant element becomes associated with aplurality of endophytes through delayed exposure. For example, the soilin which a plant element is to be introduced is first treated with acomposition comprising a plurality of endophytes. In another example,the area around the plant or plant element is exposed to a formulationcomprising a plurality of endophytes, and the plant element becomessubsequently associated with the endophytes due to movement of soil,air, water, insects, mammals, human intervention, or other methods.

The plant element can be obtained from any agricultural plant. In someembodiments, the plant element of the first plant is from amonocotyledonous plant. For example, the plant element of the firstplant is from a cereal plant. The plant element of the first plant canbe selected from the group consisting of a maize seed, a wheat seed, abarley seed, a rice seed, a sugarcane seed, a maize root, a wheat root,a barley root, a sugarcane root, a rice root, a maize leaf, a wheatleaf, a barley leaf, a sugarcane leaf, or a rice leaf. In an alternativeembodiment, the plant element of the first plant is from adicotyledonous plant. The plant element of the first plant can beselected from the group consisting of a cotton seed, a tomato seed, acanola seed, a pepper seed, a soybean seed, a cotton root, a tomatoroot, a canola root, a pepper root, a soybean root, a cotton leaf, atomato leaf, a canola leaf, a pepper leaf, or a soybean leaf. In stillanother embodiment, the plant element of the first plant can be from agenetically modified plant. In other embodiments, the plant element ofthe first plant can be a hybrid plant element.

The synthetic combination can comprise a plant element of the firstplant which is surface-sterilized prior to combining with a plurality ofendophytes. Such pre-treatment prior to coating the seed with endophytesremoves the presence of other microbes which may interfere with theoptimal colonization, growth and/or function of the endophytes. Surfacesterilization of seeds can be accomplished without killing the seeds asdescribed herein.

A single endophyte strain or a plurality of endophytes is intended to beuseful in the improvement of agricultural plants, and as such, may beformulated with other compositions as part of an agriculturallycompatible carrier. It is contemplated that such carriers can include,but not be limited to: seed treatment, root treatment, foliar treatment,soil treatment. The carrier composition with a plurality of endophytes,may be prepared for agricultural application as a liquid, a solid, or agas formulation. Application to the plant may be achieved, for example,as a powder for surface deposition onto plant leaves, as a spray to thewhole plant or selected plant element, as part of a drip to the soil orthe roots, or as a coating onto the seed prior to planting. Suchexamples are meant to be illustrative and not limiting to the scope ofthe invention.

In some embodiments, the present invention contemplates plant elementscomprising a single endophyte strain or a plurality of endophytes, andfurther comprising a formulation. The formulation useful for theseembodiments generally comprises at least one member selected from thegroup consisting of an agriculturally compatible carrier, a tackifier, amicrobial stabilizer, a fungicide, an antibacterial agent, an herbicide,a nematicide, an insecticide, a plant growth regulator, a rodenticide,and a nutrient.

In some cases, a single endophyte strain or a plurality of endophytes ismixed with an agriculturally compatible carrier. The carrier can be asolid carrier or liquid carrier. The carrier may be any one or more of anumber of carriers that confer a variety of properties, such asincreased stability, wettability, or dispersability. Wetting agents suchas natural or synthetic surfactants, which can be nonionic or ionicsurfactants, or a combination thereof can be included in a compositionof the invention. Water-in-oil emulsions can also be used to formulate acomposition that includes a plurality of endophytes. Suitableformulations that may be prepared include wettable powders, granules,gels, agar strips or pellets, thickeners, and the like,microencapsulated particles, and the like, liquids such as aqueousflowables, aqueous suspensions, water-in-oil emulsions, etc. Theformulation may include grain or legume products, for example, groundgrain or beans, broth or flour derived from grain or beans, starch,sugar, or oil.

In some embodiments, the agricultural carrier may be soil or plantgrowth medium. Other agricultural carriers that may be used includefertilizers, plant-based oils, humectants, or combinations thereof.Alternatively, the agricultural carrier may be a solid, such asdiatomaceous earth, loam, silica, alginate, clay, bentonite,vermiculite, seed cases, other plant and animal products, orcombinations, including granules, pellets, or suspensions. Mixtures ofany of the aforementioned ingredients are also contemplated as carriers,such as but not limited to, pesta (flour and kaolin clay), agar orflour-based pellets in loam, sand, or clay, etc. Formulations mayinclude food sources for the cultured organisms, such as barley, rice,or other biological materials such as seed, leaf, root, plant elements,sugar cane bagasse, hulls or stalks from grain processing, ground plantmaterial or wood from building site refuse, sawdust or small fibers fromrecycling of paper, fabric, or wood. Other suitable formulations will beknown to those skilled in the art.

In some embodiments, the formulation can comprise a tackifier oradherent. Such agents are useful for combining the microbial populationof the invention with carriers that can contain other compounds (e.g.,control agents that are not biologic), to yield a coating composition.Such compositions help create coatings around the plant or plant elementto maintain contact between the microbe and other agents with the plantor plant part. In some embodiments, adherents are selected from thegroup consisting of: alginate, gums, starches, lecithins, formononetin,polyvinyl alcohol, alkali formononetinate, hesperetin, polyvinylacetate, cephalins, Gum Arabic, Xanthan Gum, carragennan, PGA, otherbiopolymers, Mineral Oil, Polyethylene Glycol (PEG), Polyvinylpyrrolidone (PVP), Arabino-galactan, Methyl Cellulose, PEG 400,Chitosan, Polyacrylamide, Polyacrylate, Polyacrylonitrile, Glycerol,Triethylene glycol, Vinyl Acetate, Gellan Gum, Polystyrene, Polyvinyl,Carboxymethyl cellulose, Gum Ghatti, and polyoxyethylene-polyoxybutyleneblock copolymers. Other examples of adherent compositions that can beused in the synthetic preparation include those described in EP 0818135,CA 1229497, WO 2013090628, EP 0192342, WO 2008103422 and CA 1041788,each of which is incorporated herein by reference in its entirety.

It is also contemplated that the formulation may further comprise ananti-caking agent.

The formulation can also contain a surfactant, wetting agent,emulsifier, stabilizer, or anti-foaming agent. Non-limiting examples ofsurfactants include nitrogen-surfactant blends such as Prefer 28(Cenex), Surf-N(US), Inhance (Brandt), P-28 (Wilfarm) and Patrol(Helena); esterified seed oils include Sun-It II (AmCy), MSO (UAP),Scoil (Agsco), Hasten (Wilfarm) and Mes-100 (Drexel); andorgano-silicone surfactants include Silwet L77 (UAP), Silikin (Terra),Dyne-Amic (Helena), Kinetic (Helena), Sylgard 309 (Wilbur-Ellis) andCentury (Precision), polysorbate 20, polysorbate 80, Tween 20, Tween 80,Scattics, Alktest TW20, Canarcel, Peogabsorb 80, Triton X-100, Conco NI,Dowfax 9N, Igebapl CO, Makon, Neutronyx 600, Nonipol NO, Plytergent B,Renex 600, Solar NO, Sterox, Serfonic N, T-DET-N, Tergitol NP, Triton N,IGEPAL CA-630, Nonident P-40, and Pluronic. In some embodiments, thesurfactant is present at a concentration of between 0.01% v/v to 10%v/v. In other embodiments, the surfactant is present at a concentrationof between 0.1% v/v to 1% v/v. An example of an anti-foaming agent isAntifoam-C.

In certain cases, the formulation includes a microbial stabilizer. Suchan agent can include a desiccant. As used herein, a “desiccant” caninclude any compound or mixture of compounds that can be classified as adesiccant regardless of whether the compound or compounds are used insuch concentrations that they in fact have a desiccating effect on theliquid inoculant. Such desiccants are ideally compatible with theendophytes used, and should promote the ability of the microbialpopulation to survive application on the plant elements and to survivedesiccation. Examples of suitable desiccants include one or more oftrehalose, sucrose, glycerol, and Methylene glycol. Other suitabledesiccants include, but are not limited to, non-reducing sugars andsugar alcohols (e.g., mannitol or sorbitol). The amount of desiccantintroduced into the formulation can range from about 5% to about 50% byweight/volume, for example, between about 10% to about 40%, betweenabout 15% and about 35%, or between about 20% and about 30%.

In some cases, it is advantageous for the formulation to contain agentssuch as a fungicide, an antibacterial agent, an herbicide, a nematicide,an insecticide, a plant growth regulator, a rodenticide, a bactericide,a virucide, and a nutrient. Such agents are ideally compatible with theagricultural plant element or seedling onto which the formulation isapplied (e.g., it should not be deleterious to the growth or health ofthe plant). Furthermore, the agent is ideally one which does not causesafety concerns for human, animal or industrial use (e.g., no safetyissues, or the compound is sufficiently labile that the commodity plantproduct derived from the plant contains negligible amounts of thecompound).

In the liquid form, for example, solutions or suspensions, a pluralityof endophytes can be mixed or suspended in aqueous solutions. Suitableliquid diluents or carriers include aqueous solutions, petroleumdistillates, or other liquid carriers.

Solid compositions can be prepared by dispersing a plurality ofendophytes of the invention in and on an appropriately divided solidcarrier, such as peat, wheat, bran, vermiculite, clay, talc, bentonite,diatomaceous earth, fuller's earth, pasteurized soil, and the like. Whensuch formulations are used as wettable powders, biologically compatibledispersing agents such as non-ionic, anionic, amphoteric, or cationicdispersing and emulsifying agents can be used.

The solid carriers used upon formulation include, for example, mineralcarriers such as kaolin clay, pyrophyllite, bentonite, montmorillonite,diatomaceous earth, acid white soil, vermiculite, and pearlite, andinorganic salts such as ammonium sulfate, ammonium phosphate, ammoniumnitrate, urea, ammonium chloride, and calcium carbonate. Also, organicfine powders such as wheat flour, wheat bran, and rice bran may be used.The liquid carriers include vegetable oils such as soybean oil andcottonseed oil, glycerol, ethylene glycol, polyethylene glycol,propylene glycol, polypropylene glycol, etc.

In some embodiments, the formulation is ideally suited for coating of aplurality of endophytes onto plant elements. The plurality of endophytesis capable of conferring many agronomic benefits to the host plants. Theability to confer such benefits by coating the plurality of endophyteson the surface of plant elements has many potential advantages,particularly when used in a commercial (agricultural) scale.

A single endophyte strain or a plurality of endophytes can be combinedwith one or more of the agents described above to yield a formulationsuitable for combining with an agricultural plant element or seedling.The plurality of endophytes can be obtained from growth in culture, forexample, using a synthetic growth medium. In addition, the microbe canbe cultured on solid media, for example on petri dishes, scraped off andsuspended into the preparation. Microbes at different growth phases canbe used. For example, microbes at lag phase, early-log phase, mid-logphase, late-log phase, stationary phase, early death phase, or deathphase can be used. Endophytic spores may be used for the presentinvention, for example but not limited to: arthospores, sporangispores,conidia, chlamadospores, pycnidiospores, endospores, zoospores.

The formulations comprising a plurality of endophytes of the presentinvention typically contains between about 0.1 to 95% by weight, forexample, between about 1% and 90%, between about 3% and 75%, betweenabout 5% and 60%, between about 10% and 50% in wet weight of a pluralityof endophytes. In some embodiments, the formulation contains at leastabout 10{circumflex over ( )}2 per ml of formulation, at least about10{circumflex over ( )}3 per ml of formulation, for example, at leastabout 10{circumflex over ( )}4, at least about 10{circumflex over ( )}5,at least about 10{circumflex over ( )}6, at least about 10{circumflexover ( )}7 CFU or spores, at least about 10{circumflex over ( )}8 CFU orspores per ml of formulation. In some embodiments, the formulation beapplied to the plant element at about 10{circumflex over ( )}2 CFU/seed,between 10{circumflex over ( )}2 and 10{circumflex over ( )}3 CFU, atleast about 10{circumflex over ( )}3 CFU, between 10{circumflex over( )}3 and 10{circumflex over ( )}4 CFU, at least about 10{circumflexover ( )}4 CFU, between 10{circumflex over ( )}4 and 10{circumflex over( )}5 CFU, at least about 10{circumflex over ( )}5 CFU, between10{circumflex over ( )}5 and 10{circumflex over ( )}6 CFU, at leastabout 10{circumflex over ( )}6 CFU, between 10{circumflex over ( )}6 and10{circumflex over ( )}7 CFU, at least about 10{circumflex over ( )}7CFU, between 10{circumflex over ( )}7 and 10{circumflex over ( )}8 CFU,or even greater than 10{circumflex over ( )}8 CFU per seed.

The compositions provided herein are preferably stable. The endophytemay be shelf-stable, where at least 0.01%, of the CFU or spores areviable after storage in desiccated form (i.e., moisture content of 30%or less) for 1, 2, 3, 4, 5, 6, 7, 8, 9, 10 or greater than 10 weeks at4° C. or at room temperature. Optionally, a shelf-stable formulation isin a dry formulation, a powder formulation, or a lyophilizedformulation. In some embodiments, the formulation is formulated toprovide stability for the population of endophytes. In one embodiment,the formulation is substantially stable at temperatures between about−20° C. and about 50° C. for at least about 1, 2, 3, 4, 5, or 6 days, or1, 2, 3 or 4 weeks, or 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11 or 12 months,or one or more years. In another embodiment, the formulation issubstantially stable at temperatures between about 4° C. and about 37°C. for at least about 5, 10, 15, 20, 25, 30 or greater than 30 days.

As described above, in certain embodiments, the present inventioncontemplates the use of a single endophyte strain or a plurality ofendophytes heterologously disposed on the plant, for example, the plantelement. In certain cases, the agricultural plant may contain bacteriathat are substantially similar to, or even genetically indistinguishablefrom, the bacteria that are being applied to the plant. It is notedthat, in many cases, the bacteria that are being applied issubstantially different from the bacteria already present in severalsignificant ways. First, the bacteria that are being applied to theagricultural plant have been adapted to culture, or adapted to be ableto grow on growth media in isolation from the plant. Second, in manycases, the bacteria that are being applied are derived from a clonalorigin, rather than from a heterologous origin and, as such, can bedistinguished from the bacteria that are already present in theagricultural plant by the clonal similarity. For example, where amicrobe that has been inoculated by a plant is also present in the plant(for example, in a different tissue or portion of the plant), or wherethe introduced microbe is sufficiently similar to a microbe that ispresent in some of the plants (or portion of the plant, including plantelements), it is still possible to distinguish between the inoculatedmicrobe and the native microbe by distinguishing between the two microbetypes on the basis of their epigenetic status (e.g., the bacteria thatare applied, as well as their progeny, would be expected to have a muchmore uniform and similar pattern of cytosine methylation of its genome,with respect to the extent and/or location of methylation).

It is, of course, also possible to provide a coating with additionalmicroorganisms (either the same or different as the endophyte that wasinoculated). Therefore, according to another embodiment of the presentinvention, the obtained plant seed containing microorganisms istherefore subjected to a further seed impregnation step.

Once coated with the endophyte formulation, the seeds can be mixed andallowed to dry before germination occurs.

Endophytes Compatible with Agrichemicals

In certain embodiments, the single endophyte strain or the plurality ofendophytes is selected on the basis of its compatibility with commonlyused agrichemicals. As mentioned earlier, plants, particularlyagricultural plants, can be treated with a vast array of agrichemicals,including fungicides, biocides (anti-complex agents), herbicides,insecticides, nematicides, rodenticides, fertilizers, and other agents.

In some cases, it can be important for the single endophyte strain orthe plurality of endophytes to be compatible with agrichemicals,particularly those with anticomplex properties, in order to persist inthe plant although, as mentioned earlier, there are many suchanticomplex agents that do not penetrate the plant, at least at aconcentration sufficient to interfere with the endophytes. Therefore,where a systemic anticomplex agent is used in the plant, compatibilityof the endophytes to be inoculated with such agents will be an importantcriterion.

Fungicides

In some embodiments, the control agent is a fungicide. As used herein, afungicide is any compound or agent (whether chemical or biological) thatcan either inhibit the growth of a fungus or kill a fungus. In thatsense, a “fungicide”, as used herein, encompasses compounds that may befungistatic or fungicidal. As used herein, the fungicide can be aprotectant, or agents that are effective predominantly on the seedsurface, providing protection against seed surface-borne pathogens andproviding some level of control of soil-borne pathogens. Non-limitingexamples of protectant fungicides include captan, maneb, thiram, orfludioxonil.

The fungicide can be a systemic fungicide, which can be absorbed intothe emerging seedling and inhibit or kill the fungus inside host planttissues. Systemic fungicides used for seed treatment include, but arenot limited to the following: azoxystrobin, carboxin, mefenoxam,metalaxyl, thiabendazole, trifloxystrobin, and various triazolefungicides, including difenoconazole, ipconazole, tebuconazole, andtriticonazole. Mefenoxam and metalaxyl are primarily used to target thewater mold fungi Pythium and Phytophthora. Some fungicides are preferredover others, depending on the plant species, either because of subtledifferences in sensitivity of the pathogenic fungal species, or becauseof the differences in the fungicide distribution or sensitivity of theplants. In some embodiments, the endophyte is compatible with at leastone of the fungicides selected from the group consisting of:2-(thiocyanatomethylthio)-benzothiazole, 2-phenylphenol,8-hydroxyquinoline sulfate, ametoctradin, amisulbrom, antimycin,Ampelomyces quisqualis, azaconazole, azoxystrobin, Bacillus subtilis,benalaxyl, benomyl, benthiavalicarb-isopropyl,benzylaminobenzene-sulfonate (BABS) salt, bicarbonates, biphenyl,bismerthiazol, bitertanol, bixafen, blasticidin-S, borax, Bordeauxmixture, boscalid, bromuconazole, bupirimate, calcium polysulfide,captafol, captan, carbendazim, carboxin, carpropamid, carvone,chloroneb, chlorothalonil, chlozolinate, Coniothyrium minitans, copperhydroxide, copper octanoate, copper oxychloride, copper sulfate, coppersulfate (tribasic), cuprous oxide, cyazofamid, cyflufenamid, cymoxanil,cyproconazole, cyprodinil, dazomet, debacarb, diammoniumethylenebis-(dithiocarbamate), dichlofluanid, dichlorophen, diclocymet,diclomezine, dichloran, diethofencarb, difenoconazole, difenzoquat ion,diflumetorim, dimethomorph, dimoxystrobin, diniconazole, diniconazole-M,dinobuton, dinocap, diphenylamine, dithianon, dodemorph, dodemorphacetate, dodine, dodine free base, edifenphos, enestrobin,epoxiconazole, ethaboxam, ethoxyquin, etridiazole, famoxadone,fenamidone, fenarimol, fenbuconazole, fenfuram, fenhexamid, fenoxanil,fenpiclonil, fenpropidin, fenpropimorph, fentin, fentin acetate, fentinhydroxide, ferbam, ferimzone, fluazinam, fludioxonil, flumorph,fluopicolide, fluopyram, fluoroimide, fluoxastrobin, fluquinconazole,flusilazole, flusulfamide, flutianil, flutolanil, flutriafol,fluxapyroxad, folpet, formaldehyde, fosetyl, fosetyl-aluminium,fuberidazole, furalaxyl, furametpyr, guazatine, guazatine acetates,GY-81, hexachlorobenzene, hexaconazole, hymexazol, imazalil, imazalilsulfate, imibenconazole, iminoctadine, iminoctadine triacetate,iminoctadine tris(albesilate), ipconazole, iprobenfos, iprodione,iprovalicarb, isoprothiolane, isopyrazam, isotianil, kasugamycin,kasugamycin hydrochloride hydrate, kresoxim-methyl, mancopper, mancozeb,mandipropamid, maneb, mepanipyrim, mepronil, mercuric chloride, mercuricoxide, mercurous chloride, metalaxyl, mefenoxam, metalaxyl-M, metam,metam-ammonium, metam-potassium, metam-sodium, metconazole,methasulfocarb, methyl iodide, methyl isothiocyanate, metiram,metominostrobin, metrafenone, mildiomycin, myclobutanil, nabam,nitrothal-isopropyl, nuarimol, octhilinone, ofurace, oleic acid (fattyacids), orysastrobin, oxadixyl, oxine-copper, oxpoconazole fumarate,oxycarboxin, pefurazoate, penconazole, pencycuron, penflufen,pentachlorophenol, pentachlorophenyl laurate, penthiopyrad,phenylmercury acetate, phosphonic acid, phthalide, picoxystrobin,polyoxin B, polyoxins, polyoxorim, potassium bicarbonate, potassiumhydroxyquinoline sulfate, probenazole, prochloraz, procymidone,propamocarb, propamocarb hydrochloride, propiconazole, propineb,proquinazid, prothioconazole, pyraclostrobin, pyrametostrobin,pyraoxystrobin, pyrazophos, pyribencarb, pyributicarb, pyrifenox,pyrimethanil, pyroquilon, quinoclamine, quinoxyfen, quintozene,Reynoutria sachalinensis extract, sedaxane, silthiofam, simeconazole,sodium 2-phenylphenoxide, sodium bicarbonate, sodiumpentachlorophenoxide, spiroxamine, sulfur, SYP-Z071, SYP-Z048, tar oils,tebuconazole, tebufloquin, tecnazene, tetraconazole, thiabendazole,thifluzamide, thiophanate-methyl, thiram, tiadinil, tolclofos-methyl,tolylfluanid, triadimefon, triadimenol, triazoxide, tricyclazole,tridemorph, trifloxystrobin, triflumizole, triforine, triticonazole,validamycin, valifenalate, valiphenal, vinclozolin, zineb, ziram,zoxamide, Candida oleophila, Fusarium oxysporum, Gliocladium spp.,Phlebiopsis gigantea, Streptomyces griseoviridis, Trichoderma spp.,(RS)—N-(3,5-dichlorophenyl)-2-(methoxymethyl)-succinimide,1,2-dichloropropane, 1,3-dichloro-1,1,3,3-tetrafluoroacetone hydrate,1-chloro-2,4-dinitronaphthalene, 1-chloro-2-nitropropane,2-(2-heptadecyl-2-imidazolin-1-yl)ethanol,2,3-dihydro-5-phenyl-1,4-dithi-ine 1,1,4,4-tetraoxide,2-methoxyethylmercury acetate, 2-methoxyethylmercury chloride,2-methoxyethylmercury silicate, 3-(4-chlorophenyl)-5-methylrhodanine,4-(2-nitroprop-1-enyl)phenyl thiocyanateme, ampropylfos, anilazine,azithiram, barium polysulfide, Bayer 32394, benodanil, benquinox,bentaluron, benzamacril; benzamacril-isobutyl, benzamorf, binapacryl,bis(methylmercury) sulfate, bis(tributyltin) oxide, buthiobate, cadmiumcalcium copper zinc chromate sulfate, carbamorph, CECA, chlobenthiazone,chloraniformethan, chlorfenazole, chlorquinox, climbazole, cyclafuramid,cypendazole, cyprofuram, decafentin, dichlone, dichlozoline,diclobutrazol, dimethirimol, dinocton, dinosulfon, dinoterbon,dipyrithione, ditalimfos, dodicin, drazoxolon, EBP, ESBP, etaconazole,etem, ethirim, fenaminosulf, fenapanil, fenitropan, 5-fluorocytosine andprofungicides thereof, fluotrimazole, furcarbanil, furconazole,furconazole-cis, furmecyclox, furophanate, glyodine, griseofulvin,halacrinate, Hercules 3944, hexylthiofos, ICIA0858, isopamphos,isovaledione, mebenil, mecarbinzid, metazoxolon, methfuroxam,methylmercury dicyandiamide, metsulfovax, milneb, mucochloric anhydride,myclozolin, N-3,5-dichlorophenyl-succinimide,N-3-nitrophenylitaconimide, natamycin,N-ethylmercurio-4-toluenesulfonanilide, nickelbis(dimethyldithiocarbamate), OCH, phenylmercurydimethyldithiocarbamate, phenylmercury nitrate, phosdiphen, picolinamideUK-2A and derivatives thereof, prothiocarb; prothiocarb hydrochloride,pyracarbolid, pyridinitril, pyroxychlor, pyroxyfur, quinacetol;quinacetol sulfate, quinazamid, quinconazole, rabenzazole,salicylanilide, S SF-109, sultropen, tecoram, thiadifluor, thicyofen,thiochlorfenphim, thiophanate, thioquinox, tioxymid, triamiphos,triarimol, triazbutil, trichlamide, urbacid, XRD-563, and zarilamide,IK-1140. In still another embodiment, an endophyte that is compatiblewith an antibacterial compound is used for the methods described herein.For example, the endophyte is compatible with at least one of theantibiotics selected from the group consisting of: Amikacin, Gentamicin,Kanamycin, Neomycin, Netilmicin, Tobramycin, Paromomycin, Spectinomycin,Geldanamycin, Herbimycin, Rifaximin, streptomycin, Loracarbef,Ertapenem, Doripenem, Imipenem/Cilastatin, Meropenem, Cefadroxil,Cefazolin, Cefalotin or Cefalothin, Cefalexin, Cefaclor, Cefamandole,Cefoxitin, Cefprozil, Cefuroxime, Cefixime, Cefdinir, Cefditoren,Cefoperazone, Cefotaxime, Cefpodoxime, Ceftazidime, Ceftibuten,Ceftizoxime, Ceftriaxone, Cefepime, Ceftaroline fosamil, Ceftobiprole,Teicoplanin, Vancomycin, Telavancin, Clindamycin, Lincomycin,Daptomycin, Azithromycin, Clarithromycin, Dirithromycin, Erythromycin,Roxithromycin, Troleandomycin, Telithromycin, Spiramycin, Aztreonam,Furazolidone, Nitrofurantoin, Linezolid, Posizolid, Radezolid,Torezolid, Amoxicillin, Ampicillin, Azlocillin, Carbenicillin,Cloxacillin, Dicloxacillin, Flucloxacillin, Mezlocillin, Methicillin,Nafcillin, Oxacillin, Penicillin G, Penicillin V, Piperacillin,Penicillin G, Temocillin, Ticarcillin, Amoxicillin/clavulanate,Ampicillin/sulbactam, Piperacillin/tazobactam, Ticarcillin/clavulanate,Bacitracin, Colistin, Polymyxin B, Ciprofloxacin, Enoxacin,Gatifloxacin, Levofloxacin, Lomefloxacin, Moxifloxacin, Nalidixic acid,Norfloxacin, Ofloxacin, Trovafloxacin, Grepafloxacin, Sparfloxacin,Temafloxacin, Mafenide, Sulfacetamide, Sulfadiazine, Silversulfadiazine, Sulfadimethoxine, Sulfamethizole, Sulfamethoxazole,Sulfanilimide (archaic), Sulfasalazine, Sulfisoxazole,Trimethoprim-Sulfamethoxazole (Co-trimoxazole) (TMP-SMX),Sulfonamidochrysoidine (archaic), Demeclocycline, Doxycycline,Minocycline, Oxytetracycline, Tetracycline, Clofazimine, Dapsone,Capreomycin, Cycloserine, Ethambutol, Ethionamide, Isoniazid,Pyrazinamide, Rifampicin (Rifampin in US), Rifabutin, Rifapentine,Streptomycin, Arsphenamine, Chloramphenicol, Fosfomycin, Fusidic acid,Metronidazole, Mupirocin, Platensimycin, Quinupristin/Dalfopristin,Thiamphenicol, Tigecycline, Tinidazole, and Trimethoprim.

A fungicide can be a biological control agent, such as a bacterium orfungus. Such organisms may be parasitic to the pathogenic fungi, orsecrete toxins or other substances which can kill or otherwise preventthe growth of fungi. Any type of fungicide, particularly ones that arecommonly used on plants, can be used as a control agent in a seedcomposition.

Antibacterial Agents

In some cases, the seed coating composition comprises a control agentwhich has antibacterial properties. In some embodiments, the controlagent with antibacterial properties is selected from the compoundsdescribed herein elsewhere. In other embodiments, the compound isStreptomycin, oxytetracycline, oxolinic acid, or gentamicin.

Plant Growth Regulators

The seed coat composition can further comprise a plant growth regulator.In some embodiments, the plant growth regulator is selected from thegroup consisting of: Abscisic acid, amidochlor, ancymidol,6-benzylaminopurine, brassinolide, butralin, chlormequat (chlormequatchloride), choline chloride, cyclanilide, daminozide, dikegulac,dimethipin, 2,6-dimethylpuridine, ethephon, flumetralin, flurprimidol,fluthiacet, forchlorfenuron, gibberellic acid, inabenfide,indole-3-acetic acid, maleic hydrazide, mefluidide, mepiquat (mepiquatchloride), naphthaleneacetic acid, N-6-benzyladenine, paclobutrazol,prohexadione (prohexadione-calcium), prohydrojasmon, thidiazuron,triapenthenol, tributyl phosphorotrithioate, 2,3,5-tri-iodobenzoic acid,trinexapac-ethyl and uniconazole. Other examples of antibacterialcompounds which can be used as part of a seed coating compositioninclude those based on dichlorophene and benzylalcohol hemi formal(Proxel® from ICI or Acticide® RS from Thor Chemie and Kathon® MK fromRohm & Haas) and isothiazolinone derivatives such asalkylisothiazolinones and benzisothiazolinones (Acticide® MBS from ThorChemie). Other plant growth regulators that can be incorporated seedcoating compositions are described in US 2012/0108431, which isincorporated by reference in its entirety.

Nematicides

Preferred nematode-antagonistic biocontrol agents include ARF18;Arthrobotrys spp.; Chaetomium spp.; Cylindrocarpon spp.; Exophilia spp.;Fusarium spp.; Gliocladium spp.; Hirsutella spp.; Lecanicillium spp.;Monacrosporium spp.; Myrothecium spp.; Neocosmospora spp.; Paecilomycesspp.; Pochonia spp.; Stagonospora spp.; vesicular-arbuscular mycorrhizalfungi, Burkholderia spp.; Pasteuria spp., Brevibacillus spp.;Pseudomonas spp.; and Rhizobacteria. Particularly preferrednematode-antagonistic biocontrol agents include ARF18, Arthrobotrysoligospora, Arthrobotrys dactyloides, Chaetomium globosum,Cylindrocarpon heteronema, Exophilia jeanselmei, Exophilia pisciphila,Fusarium aspergilus, Fusarium solani, Gliocladium catenulatum,Gliocladium roseum, Gliocladium vixens, Hirsutella rhossiliensis,Hirsutella minnesotensis, Lecanicillium lecanii, Monacrosporiumdrechsleri, Monacrosporium gephyropagum, Myrotehcium verrucaria,Neocosmospora vasinfecta, Paecilomyces lilacinus, Pochoniachlamydosporia, Stagonospora heteroderae, Stagonospora phaseoli,vesicular-arbuscular mycorrhizal fungi, Burkholderia cepacia, Pasteuriapenetrans, Pasteuria thornei, Pasteuria nishizawae, Pasteuria ramosa,Pasteuria usage, Brevibacillus laterosporus strain G4, Pseudomonasfluorescens and Rhizobacteria.

Nutrients

In other embodiments, the seed coating composition can comprise anutrient. The nutrient can be selected from the group consisting of anitrogen fertilizer including, but not limited to Urea, Ammoniumnitrate, Ammonium sulfate, Non-pressure nitrogen solutions, Aquaammonia, Anhydrous ammonia, Ammonium thiosulfate, Sulfur-coated urea,Urea-formaldehydes, IBDU, Polymer-coated urea, Calcium nitrate,Ureaform, and Methylene urea, phosphorous fertilizers such as Diammoniumphosphate, Monoammonium phosphate, Ammonium polyphosphate, Concentratedsuperphosphate and Triple superphosphate, and potassium fertilizers suchas Potassium chloride, Potassium sulfate, Potassium-magnesium sulfate,Potassium nitrate. Such compositions can exist as free salts or ionswithin the seed coat composition. Alternatively, nutrients/fertilizerscan be complexed or chelated to provide sustained release over time.

Rodenticides

Rodents such as mice and rats cause considerable economical damage byeating and soiling planted or stored seeds. Moreover, mice and ratstransmit a large number of infectious diseases such as plague, typhoid,leptospirosis, trichinosis and salmonellosis. Anticoagulants such ascoumarin and indandione derivatives play an important role in thecontrol of rodents. These active ingredients are simple to handle,relatively harmless to humans and have the advantage that, as the resultof the delayed onset of the activity, the animals being controlledidentify no connection with the bait that they have ingested, thereforedo not avoid it. This is an important aspect in particular in socialanimals such as rats, where individuals act as tasters. In someembodiments, the seed coating composition comprises a rodenticideselected from the group of substances consisting of2-isovalerylindan-1,3-dione, 4-(quinoxalin-2-ylamino)benzenesulfonamide,alpha-chlorohydrin, aluminum phosphide, antu, arsenous oxide, bariumcarbonate, bisthiosemi, brodifacoum, bromadiolone, bromethalin, calciumcyanide, chloralose, chlorophacinone, cholecalciferol, coumachlor,coumafuryl, coumatetralyl, crimidine, difenacoum, difethialone,diphacinone, ergocalciferol, flocoumafen, fluoroacetamide, flupropadine,flupropadine hydrochloride, hydrogen cyanide, iodomethane, lindane,magnesium phosphide, methyl bromide, norbormide, phosacetim, phosphine,phosphorus, pindone, potassium arsenite, pyrinuron, scilliroside, sodiumarsenite, sodium cyanide, sodium fluoroacetate, strychnine, thalliumsulfate, warfarin and zinc phosphide.

Compatibility

In some embodiments, a single endophyte strain or a plurality ofendophytes that are compatible with agrichemicals can be used toinoculate the plants according to the methods described herein. In eachcase below, each single endophyte strain or each type of endophyte usedin a plurality of endophytes can be tested for compatibility on theirown or as the plurality. Endophytes that are compatible withagriculturally employed anticomplex agents can be isolated by plating aculture of endophytes on a petri dish comprising an effectiveconcentration of the anticomplex agent, and isolating colonies ofendophytes that are compatible with the anticomplex agent. In otherembodiments, a plurality of endophytes that are compatible with ananticomplex agent are used for the methods described herein.

In some embodiments, the endophytes of the present invention displaytolerance to an agrichemical selected from the group consisting of:Aeris®, Avicta® DuoCot 202, Cruiser®, Syntenta CCB® (A), Clariva®,Albaugh, Dynasty®, Apron®, Maxim®, Gaucho®, Provoke® ST, Syngenta CCB®,Trilex®, WG Purple, WG Silver, Azoxystrobin, Carboxin, Difenoconazole,Fludioxonil, fluxapyroxad, Ipconazole, Mefenoxam, Metalaxyl,Myclobutanil, Penflufen, pyraclostrobin, Sedaxane, TCMTB, Tebuconazole,Thiram, Triadimenol (Baytan®), Trifloxystrobin, Triticonazole,Tolclofos-methyl, PCNB, Abamectin, Chlorpyrifos, Clothianidin,Imidacloprid, Thiamethoxam, and Thiodicarb.

Bactericide-compatible endophytes can also be isolated by selection onliquid medium. The culture of endophytes can be plated on petri disheswithout any forms of mutagenesis; alternatively, endophytes can bemutagenized using any means known in the art. For example, endophytecultures can be exposed to UV light, gamma-irradiation, or chemicalmutagens such as ethylmethanesulfonate (EMS), ethidium bromide (EtBr)dichlovos (DDVP, methyl methane sulphonale (MMS), triethylphosphate(TEP), trimethylphosphate (TMP), nitrous acid, or DNA base analogs,prior to selection on fungicide comprising media. Finally, where themechanism of action of a particular bactericide is known, the targetgene can be specifically mutated (either by gene deletion, genereplacement, site-directed mutagenesis, etc.) to generate a plurality ofendophytes that are resilient against that particular chemical. It isnoted that the above-described methods can be used to isolate endophytesthat are compatible with both bacteriostatic and bactericidal compounds.

It will also be appreciated by one skilled in the art that a plant maybe exposed to multiple types of anticomplex compounds, eithersimultaneously or in succession, for example at different stages ofplant growth. Where the target plant is likely to be exposed to multipleanticomplex agents, a plurality of endophytes that are compatible withmany or all of these agrichemicals can be used to inoculate the plant.Endophytes that are compatible with several agents can be isolated, forexample, by serial selection. Endophytes that are compatible with thefirst agent can be isolated as described above (with or without priormutagenesis). A culture of the resulting endophytes can then be selectedfor the ability to grow on liquid or solid media comprising the secondagent (again, with or without prior mutagenesis). Colonies isolated fromthe second selection are then tested to confirm its compatibility toboth agents.

Likewise, endophytes that are compatible to biocides (includingherbicides such as glyphosate or anticomplex compounds, whetherbacteriostatic or bactericidal) that are agriculturally employed can beisolated using methods similar to those described for isolatingcompatible endophytes. In some embodiments, mutagenesis of theendophytes can be performed prior to selection with an anticomplexagent. In other embodiments, selection is performed on the endophyteswithout prior mutagenesis. In still another embodiment, serial selectionis performed on endophytes: the endophytes are first selected forcompatibility to a first anticomplex agent. The isolated compatibleendophytes are then cultured and selected for compatibility to thesecond anticomplex agent. Any colony thus isolated is tested forcompatibility to each, or both anticomplex agents to confirmcompatibility with these two agents.

Compatibility with an antimicrobial agent can be determined by a numberof means known in the art, including the comparison of the minimalinhibitory concentration (MIC) of the unmodified and modifiedendophytes. Therefore, in some embodiments, the present inventiondiscloses modified endophytes, wherein the endophytes are modified suchthat they exhibits at least 3 fold greater, for example, at least 5 foldgreater, between 5 and 10 fold greater, at least 10 fold greater,between 10 and 20 fold greater, at least 20 fold greater, between 20 and30 fold greater, at least 30 fold greater or more MIC to anantimicrobial agent when compared with the unmodified endophytes.

In some embodiments, disclosed herein are endophytes with enhancedcompatibility to the herbicide glyphosate. In some embodiments, theendophytes have a doubling time in growth medium comprising least 1 mMglyphosate, for example, between 1 mM and 2 mM glyphosate, at least 2 mMglyphosate, between 2 mM and 5 mM glyphosate, at least 5 mM glyphosate,between 5 mM and 10 mM glyphosate, at least 10 mM glyphosate, between 10mM and 15 mM glyphosate, at least 15 mM glyphosate or more, that is nomore than 250%, between 250% and 100%, for example, no more than 200%,between 200% and 175%, no more than 175%, between 175% and 150%, no morethan 150%, between 150% and 125%, or no more than 125%, of the doublingtime of the endophytes in the same growth medium comprising noglyphosate. In some embodiments, the endophytes have a doubling time ingrowth medium comprising 5 mM glyphosate that is no more than 150% thedoubling time of the endophytes in the same growth medium comprising noglyphosate.

In other embodiments, the endophytes have a doubling time in a planttissue comprising at least 10 ppm glyphosate, for example, between 10and 15 ppm, at least 15 ppm glyphosate, between 15 and 10 ppm, at least20 ppm glyphosate, between 20 and 30 ppm, at least 30 ppm glyphosate,between 30 and 40 ppm, at least 40 ppm glyphosate or more, that is nomore than 250%, between 250% and 200%, for example, no more than 200%,between 200% and 175%, no more than 175%, between 175% and 150%, no morethan 150%, between 150% and 125%, of the doubling time of the endophytesin a reference plant tissue comprising no glyphosate. In someembodiments, the endophytes have a doubling time in a plant tissuecomprising 40 ppm glyphosate that is no more than 150% the doubling timeof the endophytes in a reference plant tissue comprising no glyphosate.

The selection process described above can be repeated to identifyisolates of endophytes that are compatible with a multitude of agents.

Candidate isolates can be tested to ensure that the selection foragrichemical compatibility did not result in loss of a desiredbioactivity. Isolates of endophytes that are compatible with commonlyemployed agents can be selected as described above. The resultingcompatible endophytes can be compared with the parental endophytes onplants in its ability to promote germination.

The agrichemical compatible endophytes generated as described above canbe detected in samples. For example, where a transgene was introduced torender the endophytes compatible with the agrichemical(s), the transgenecan be used as a target gene for amplification and detection by PCR. Inaddition, where point mutations or deletions to a portion of a specificgene or a number of genes results in compatibility with theagrichemical(s), the unique point mutations can likewise be detected byPCR or other means known in the art. Such methods allow the detection ofthe endophytes even if they is no longer viable. Thus, commodity plantproducts produced using the agrichemical compatible endophytes describedherein can readily be identified by employing these and related methodsof nucleic acid detection.

Populations of Plant Elements

The synthetic combinations of the present invention may be confinedwithin an object selected from the group consisting of: bottle, jar,ampule, package, vessel, bag, box, bin, envelope, carton, container,silo, shipping container, truck bed, and case. In a particularembodiment, the population of plant elements is packaged in a bag orcontainer suitable for commercial sale. For example, a bag contains aunit weight or count of the plant elements comprising a plurality ofendophytes as described herein, and further comprises a label. In oneembodiment, the bag or container contains at least 100 plant elements,between 100 and 1,000 plant elements, 1,000 plant elements, between1,000 and 5,000 plant elements, for example, at least 5,000 plantelements, between 5,000 and 10,000 plant elements, at least 10,000 plantelements, between 10,000 and 20,000 plant elements, at least 20,000plant elements, between 20,000 and 30,000 plant elements, at least30,000 plant elements, between 30,000 and 50,000 plant elements, atleast 50,000 plant elements, between 50,000 and 70,000 plant elements,at least 70,000 plant elements, between 70,000 and 80,000 plantelements, at least 80,000 plant elements, between 80,000 and 90,000, atleast 90,000 plant elements or more. In another embodiment, the bag orcontainer can comprise a discrete weight of plant elements, for example,at least 1 lb, between 1 and 2 lbs, at least 2 lbs, between 2 and 5 lbs,at least 5 lbs, between 5 and 10 lbs, at least 10 lbs, between 10 and 30lbs, at least 30 lbs, between 30 and 50 lbs, at least 50 lbs, between 50and 70 lmbs, at least 70 lbs or more. The label can contain additionalinformation, for example, the information selected from the groupconsisting of: net weight, lot number, geographic origin of the plantelements, test date, germination rate, inert matter content, and theamount of noxious weeds, if any. Suitable containers or packages includethose traditionally used in plant element commercialization. Theinvention also contemplates other containers with more sophisticatedstorage capabilities (e.g., with microbiologically tight wrappings orwith gas- or water-proof containments).

In some cases, a sub-population of plant elements comprising a pluralityof endophytes is further selected on the basis of increased uniformity,for example, on the basis of uniformity of microbial population. Forexample, individual plant elements of pools collected from individualcobs, individual plants, individual plots (representing plantsinoculated on the same day) or individual fields can be tested foruniformity of microbial density, and only those pools meetingspecifications (e.g., at least 80% of tested plant elements have minimumdensity, as determined by quantitative methods described elsewhere) arecombined to provide the agricultural plant element sub-population.

The methods described herein can also comprise a validating step. Thevalidating step can entail, for example, growing some plant elementscollected from the inoculated plants into mature agricultural plants,and testing those individual plants for uniformity. Such validating stepcan be performed on individual plant elements collected from cobs,individual plants, individual plots (representing plants inoculated onthe same day) or individual fields, and tested as described above toidentify pools meeting the required specifications.

In some embodiments, methods described herein include planting asynthetic composition described herein. Suitable planters include an airseeder and/or fertilizer apparatus used in agricultural operations toapply particulate materials including one or more of the following,seed, fertilizer and/or inoculants, into soil during the plantingoperation. Seeder/fertilizer devices can include a tool bar havingground-engaging openers thereon, behind which is towed a wheeled cartthat includes one or more containment tanks or bins and associatedmetering means to respectively contain and meter therefrom particulatematerials.

In certain embodiments, a composition described herein may be in theform of a liquid, a slurry, a solid, or a powder (wettable powder or drypowder). In another embodiment, a composition may be in the form of aseed coating. Compositions in liquid, slurry, or powder (e.g., wettablepowder) form may be suitable for coating plant elements. When used tocoat plant elements, the composition may be applied to the plantelements and allowed to dry. In embodiments wherein the composition is apowder (e.g., a wettable powder), a liquid, such as water, may need tobe added to the powder before application to a seed.

In still another embodiment, the methods can include introducing intothe soil an inoculum of one or more of the endophyte populationsdescribed herein. Such methods can include introducing into the soil oneor more of the compositions described herein. The inoculum(s) orcompositions may be introduced into the soil according to methods knownto those skilled in the art. Non-limiting examples include in-furrowintroduction, spraying, coating seeds, foliar introduction, etc. In aparticular embodiment, the introducing step comprises in-furrowintroduction of the inoculum or compositions described herein.

In one embodiment, plant elements may be treated with composition(s)described herein in several ways but preferably via spraying ordripping. Spray and drip treatment may be conducted by formulatingcompositions described herein and spraying or dripping thecomposition(s) onto a seed(s) via a continuous treating system (which iscalibrated to apply treatment at a predefined rate in proportion to thecontinuous flow of seed), such as a drum-type of treater. Batch systems,in which a predetermined batch size of seed and composition(s) asdescribed herein are delivered into a mixer, may also be employed.

In another embodiment, the treatment entails coating plant elements. Onesuch process involves coating the inside wall of a round container withthe composition(s) described herein, adding plant elements, thenrotating the container to cause the plant elements to contact the walland the composition(s), a process known in the art as “containercoating”. Plant elements can be coated by combinations of coatingmethods. Soaking typically entails using liquid forms of thecompositions described. For example, plant elements can be soaked forabout 1 minute to about 24 hours (e.g., for at least 1 min, between 1and 5 min, 5 min, between 5 and 10 min, 10 min, between 10 and 20 min,20 min, between 20 and 40 min, 40 min, between 40 and 80 min, 80 min,between 80 min and 3 hrs, 3 hrs, between 3 hrs and 6 hrs, 6 hr, between6 hrs and 12 hrs, 12 hr, between 12 hrs and 24 hrs, or at least 24 hrs).

Throughout the specification, the word “comprise,” or variations such as“comprises” or “comprising,” will be understood to imply the inclusionof a stated integer or group of integers but not the exclusion of anyother integer or group of integers.

Although the present invention has been described in detail withreference to examples below, it is understood that various modificationscan be made without departing from the spirit of the invention. Forinstance, while the particular examples below may illustrate the methodsand embodiments described herein using a specific plant, the principlesin these examples may be applied to any agricultural crop. Therefore, itwill be appreciated that the scope of this invention is encompassed bythe embodiments of the inventions recited herein and the specificationrather than the specific examples that are exemplified below.

EXAMPLES Example 1: Cultivation-Independent Analysis of Microbial Taxain Agriculturally Relevant Seed Communities Based on Marker GeneHigh-Throughput Sequencing

Example Description

Microbial taxa found in agriculturally relevant communities wereidentified using high-throughput marker gene sequencing across severalcrops and numerous varieties of seeds.

Experimental Description

To identify core (i.e. ubiquitous) microbial taxa across seeds, we usedhigh-throughput sequencing of marker genes for bacteria, archaea, andfungi.

Cereals

2 inbred, 10 landrace, 4 teosinte corn seeds, and 4 modern and 4 wildwheat seeds were obtained. Accessions were categorized into landrace,wild, and inbred varieties based on their assessment of improvementstatus. In order to extract microbial DNA, the seeds were firststerilized in one of four different manners. Some of the seeds weresurface sterilized using 95% ethanol to reduce superficial contaminantmicrobes, then rinsed in water. Others were first soaked in sterile,DNA-free water for 48 hours to soften them, and they were surfacesterilized using 95% ethanol to reduce superficial contaminant microbes,then rinsed in water. Others were rinsed in deionized water, immersed in95% ethanol for 5 seconds, 0.5% NaOCl for 2 minutes, 70% ethanol for 2minutes, and then washed three times in deionized water for 1 minuteeach.

Grasslands

To identify microbial taxa from seeds of wild grassland plants, we usedhigh-throughput sequencing of marker genes for bacteria, archaea, andfungi. Seeds from the following wild grassland species were obtained:Big bluestem, Side oats grama, Bicknell's sedge, Short beak sedge,Canada wild rye, Virginia wild rye, June grass, Leafy satin grass,Switch grass, Little bluestem, Prairie cord grass, Prairie dropseed,Nodding wild onion, Meadow/Canada anemone, Common milkweed, Butterflyweed, Whorled milkweed, New England aster, False boneset, Tallcoreopsis, Shooting star, Pale purple coneflower, Rattlesnake master,Tall boneset, Purple joe pye weed, Biennial gaure, Prairie smoke, Falsesunflower, Rough blazing star, Wild bergamot, Horse mint, Common eveningprimrose, Wild quinine, Beardtongue, Yellow coneflower, Black-eyedSusan, Sweet black-eyed susan, Compass plant, Prairie dock, Stiffgoldenrod, Showy goldenrod, Hairy aster, Hoary vervain, Culver's root,Golden alexanders, Dogtooth daisy, Wild blue iris, Pointed broom sedge,Dark green bulrush, and Blue vervain. In order to extract microbial DNA,the seeds were first soaked in sterile, DNA-free water for 48 h tosoften them, and they were surface sterilized using 95% ethanol toreduce superficial contaminant microbes, then rinsed in water.

Fruits and Vegetables

Seeds from 22 different varieties of cabbage were obtained, includingbroccoli, cauliflower, and collards. In addition, seeds from 8 differentvarieties of lettuce, 9 varieties of melon (including cantaloupe andhoneydew), 7 varieties of onions (including cippolini, shallots, andvidalia), 4 varieties of tomatoes, one variety of toria, 4 varities ofturnip, 7 varieties of watermelon, and one variety of yellow sarcon wereobtained. For strawberries, the seeds or runner plant tissue of 9varieties were obtained. For sterilization, the seeds were first soakedin sterile, DNA-free water for 48 h to soften them, and they weresurface sterilized using 95% ethanol to reduce superficial contaminantmicrobes, then rinsed in water. Strawberry tissue was surface sterilizedusing 95% ethanol, then rinsed in water.

Oilseed

Seeds from 1 wild and 3 modern cultivars of Brassica Napus were alsoobtained. In order to extract microbial DNA, the seeds were first soakedin sterile, DNA-free water for 48 h to soften them, and they weresurface sterilized using 95% ethanol to reduce superficial contaminantmicrobes, then rinsed in water.

The seeds or tissues from all of the plants described above were thenground using a mortar and pestle treated with 95% ethanol and RNAse Away(Life Technologies, Inc., Grand Island, N.Y.) to remove contaminant DNA.DNA was extracted from the ground seeds using the PowerPlant Pro DNAextraction kit (Mo Bio Laboratories, Inc., Carlsbad, Calif.) accordingto the manufacturer's instructions. The surface wash off from certainsterilization treatments of cereal seeds was also collected and DNA wasextracted as above.

Marker genes were amplified and sequenced from the extracted DNA. Forthe bacterial and archaeal analyses, the V4 hypervariable region of the16S rRNA gene was targeted (primers 515f/806r), and for fungi, the firstinternal transcribed spacer (ITS1) region of the rRNA operon (primersITS1f/ITS2r) was targeted. The two marker genes were PCR amplifiedseparately using 35 cycles, and error-correcting 12-bp barcoded primersspecific to each sample were used to faciliate combining of samples. Toreduce the amplification of chloroplast and mitochondrial DNA, PNAclamps specific to the rRNA genes in these organelles were used. PCRreactions to amplify 16S rRNA genes followed the protocol of Lundberg etal 2013, and those to amplify ITS regions followed the protocol ofFierer et al. 2012. PCR products were quantified using the PicoGreenassay (Life Technologies, Inc., Grand Island, N.Y.), pooled in equimolarconcentrations, and cleaned using the UltraClean kit (Mo BioLaboratories, Inc., Carlsbad, Calif.). Cleaned DNA pools were sequencedon an Illumina MiSeq instrument at the University of Colorado NextGeneration Sequencing Facility.

OTU Assignment

For both 16S rRNA and ITS1 sequences, the raw sequence data werereassigned to distinct samples using a custom Python script, and qualityfiltering and OTU (i.e. operational taxonomic unit) clustering wasconducted using the UPARSE pipeline (Edgar 2013). Briefly, a de novosequence database with representative sequences for each OTU was createdusing a 97% similarity threshold, and raw reads were mapped to thisdatabase to calculate sequence counts per OTU per sample. Prior tocreating the database, sequences were quality filtered using an expectederror frequency threshold of 0.5 errors per sequence. In addition,sequences were dereplicated and singletons were removed prior tocreating the database. OTUs were provided taxonomic classificationsusing the RDP classifier (Wang et al. 2007) trained with the Greengenes(McDonald et al. 2012) and UNITE (Abarenkov et al. 2010) databases for16S rRNA and ITS sequences, respectively. To account for differences inthe variable number of sequences per sample, each sample was rarefied to1000 16S rRNA and 1000 ITS sequences per sample. OTUs classified aschloroplasts or mitochondria were discarded prior to rarefaction.

Overall differences in bacterial community composition between thecontrol and inoculated plants were evaluated using non-metricmultidimensional scaling based on Bray-Curtis dissimilarities in orderto visualize pairwise differences between sample communities.Permutational analysis of variance (PERMANOVA) was used to statisticallytest the significance of these differences. Analyses were conductedusing the vegan package in R (R Core Team 2013). To determine the OTUscontributing to overall differences among crop types, mean relativeabundances were calculated for each OTU within each crop type. Only OTUswith a mean relative abundance of 0.1% in either group were included inthis analysis.

Results

Across seeds from all plants analyzed herein, a total of 144 bacterialand 145 fungal OTUs were detected and evaluated (Table 3 and Table 4)following stringent sequence quality filtering approach. Among all OTUs,28 bacterial OTUs and 20 fungal OTUs were found to be core taxa withinseeds across plants (Table 1 and Table 2).

TABLE 3 Exemplary bacterial endophytes present in all plants. SEQ OTU_IDID NO Phylum Class Order Family Genus Species OTU_558 1 OD1 ABY1 OTU_7622 Actinobacteria Actinobacteria Actinomycetales MicrobacteriaceaeOTU_136 3 Actinobacteria Actinobacteria ActinomycetalesStreptomycetaceae Streptomyces OTU_161 4 Acunobacteria ActinobacteriaActinomycetales Corynebacteriaceae Corynebacterium OTU_309 5Actinobacteria Actinobacteria Actinomycetales CorynebacteriaceaeCorynebacterium OTU_63 6 Acunobacteria Actinobacteria ActinomycetalesGeodermatophilaceae OTU_67 7 Actinobacteria ActinobacteriaActinomycetales Sanguibacteraceae Sanguibacter OTU_1203 8 ActinobacteriaActinobacteria Actinomycetales Microbacteriaceae Rathayibacter caricisOTU_364 9 Actinobacteria Actinobacteria Actinomycetales MicrococcaceaeMicrobispora rosea OTU_130 10 Actinobacteria ActinobacteriaActinomycetales Nocardiaceae Rhodococcus fascians OTU_74 11Actinobacteria Actinobacteria Actinomycetales KineosporiaceaeKineococcus OTU_41 12 Actinobacteria Actinobacteria ActinomycetalesMicrobacteriaceae OTU_24 13 Actinobacteria ActinobacteriaActinomycetales Microbacteriaceae OTU_1230 14 ProteobacteriaAlphaproteobacteria Sphingomonadales Sphingomonadaceae OTU_30 15Proteobacteria Alphaproteobacteria Caulobacterales CaulobacteraceaeMycoplana OTU_799 16 Proteobacteria Alphaproteobacteria RhizobialesRhizobiaceae Agrobacterium OTU_101 17 Proteobacteria AlphaproteobacteriaRhizobiales Aurantimonadaceae OTU_572 18 ProteobiietcnaAlphaproteobacteria Rhizobiales Phyllobacteriaccac Mesorhizobium OTU_15319 Proteobacteria Alphaproteobacteria Rhizobiales HyphomicrobiaceaeDevosia OTU_140 20 Proteobacteria Alphaproteobacteria SphingomonadalesSphingomonadaceae Sphingomoius OTU_194 21 ProteobacteriaAlphaproteobacteria Rhizobiales Methylocystaceae OTU_158 22Proteobacteiia Alphaproteobacteria Caulobacterales CaulobacteraceaeOTU_124 23 Proteobacteria Alphaproteobacteria SphingomonadalesSphingomonadacea Sphingomonas wittichii OTU_188 24 ProteobacteriaAlphaproteobacteria Rhodospirillales Acetobacteraceae OTU_1287 25Proteobacteria Alphaproteobacteria Sphingomonadales SphingomonadaceaeNovosphingobium OTU_971 26 Proteobacteria AlphaproteobacteriaRhodobacterales Rhodobacteraceae Rhodobacter OTU_20 27 ProteobacteriaAlphaproteobacteria Rhizobiales Aurantimonadaceae OTU_57 28Proteobacteria Alphaproteobacteria Sphingomonadales SphingomonadaceaeNovosphingobium OTU_49 29 Proteobacteria Alphaproteobacteria RhizobialesMethylobacteriaceae OTU_1222 30 Proteobacteria AlphaproteobacteriaSphingomonadales Sphingomonadaceae Sphingomonas OTU_80 31 ProteobacteriaAlphaproteobacteria Sphingomonadales Sphingomonadaceae SphingomonasOTU_436 32 Proteobacteria Alphaproteobacteria SphingomonadalesSphingomonadaceae Sphingomonas OTU_1077 33 ProteobacteriaAlphaproteobacteria Rhizobiales Methylobacteriaceae Methylobacteriumadhaesivum OTU_510 34 Proteobacteria AlphaproteobacteriaRhodospirillales Rhodospirillaceae Azospirillum OTU_43 35 ProteobacteriaAlphaproteobacteria Rhizobiales Methylobacteriaceae Methylobacteriumadhaesivum OTU_65 36 Proteobacteria Alphaproteobacteria RhodospirillalesAcetobacteraceae OTU_64 37 Proteobacteria AlphaproteobacteriaSphingomonadales Sphingomonadaceae Sphingomonas wittichii OTU_27 38Proteobacteria Alphaproteobacteria Sphingomonadales SphingomonadaceaeSphingomonas OTU_47 39 Proteobacteria Alphaproteobacteria RhizobialesMethylobacteriaceae Methylobacterium OTU_15 40 ProteobacteriaAlphaproteobacteria Rhizobiales Rhizobiaceae Agrobacterium OTU_956 41Proteobacteria Alphaproteobacteria Rhizobiales MethylobacteriaceaeMethylobacterium adhaesivum OTU_21 42 Proteobacteria AlphaproteobacteriaRhizobiales Methylobacteriaceae Methylobacterium OTU_14 43Prolcobiictena Alphaproteobacteria Sphingomonadales SphingomonadaceaeSphingomonas OTU_6 44 Proteobacteria AlphaproteobacteriaSphingomonadales Sphingomonadaceae Sphingomonas OTU_1436 45Proteobacteria Alphaproteobacteria Sphingomonadales SphingomonadaceaeSphingomonas OTU_61 46 Firmicutes Bacilli Bacillales PaenibacillaceaePaenibacillus OTU_77 47 Firmicutes Bacilli LactobacillalesLeuconostocaceae Leuconostoc OTU_358 48 Firmicutes Bacilli BacillalesBacillaceae Bacillus badius OTU_353 49 Firmicutes Bacilli BacillalesPaenibacillacea Paenibacillus OTU_1250 50 Firmicutes Bacilli BacillalesPlanococcaceae Sporosarcina ginsengi OTU_84 51 Firmicutes BacilliBacillales Bacillaceae OTU_34 52 Firmicutes Bacilli BacillalesBacillaceae Bacillus cereus OTU_98 53 Firmicutes Bacilli BacillalesPaenibacillaceae Paenibacillus OTU_152 54 Firmicutes Bacilli BacillalesPaenibacillaceae Paenibacillus OTU_1178 55 Firmicutes Bacilli BacillalesPlanococcaceae Planomicrobium OTU_299 56 Firmicutes BacilliLactobacillales Leuconostocaceae Leuconostoc OTU_241 57 FirmicutesBacilli Lactobacillales Carnobacteriaceae Carnobacterium OTU_203 58Firmicutes Bacilli Lactobacillales Streptococcaceae Lactococcus OTU_2559 Firmicutes Bacilli Bacillales Paenibacillaceae OTU_17 60 FirmicutesBacilli Bacillales Bacillaceae Bacillus OTU_330 61 Firmicutes BacilliLactobacillales Lactobacillaceae OTU_211 62 Firmicutes BacilliLactobacillales Enterococcaceae Enterococcus OTU_108 63 FirmicutesBacilli Bacillales Staphylococcaceae Staphylococcus OTU_19 64 FirmicutesBacilli Bacillales Paenibacillaceae Paenibacillus amylolyticus OTU_16 65Firmicutes Bacilli Bacillales [Exiguobacteraceae] ExiguobacteriumOTU_372 66 Firmicutes Bacilli Bacillales Sporolactobacillaceae Bacillusracemilacticus OTU_222 67 Firmicutes Bacilli Bacillales BacillaceaeGeobacillus OTU_653 68 Firmicutes Bacilli Bacillales BacillaceaeBacillus endophyticus OTU_11 69 Firmicutes Bacilli BacillalesPaenibacillaceae Paenibacillus OTU_71 70 Firmicutes Bacilli BacillalesPaenibacillaceae Saccharibacillus kuerlensis OTU_13 71 FirmicutesBacilli Bacillales Bacillaceae Bacillus flexus OTU_10 72 FirmicutesBacilli Bacillales Planococcaceae Sporosarcina ginsengi OTU_118 73Proteobacteria Betaproteobacteria Burkholderiales ComamonadaceaeComamonas OTU_676 74 Proteobacteria Betaproteobacteria BurkholderialesComamonadaceae Limnohabitans OTU_1014 75 ProteobacteriaBetaproteobacteria Burkholderiales Oxalobacteraceae JanthinobacteriumOTU_26 76 Proteobacteria Betaproteobacteria BurkholderialesOxalobacteraceae OTU_182 77 Proteobacteria BetaproteobacteriaBurkholderiales Alcaligenaceae Pigmentipbaga OTU_980 78 ProteobacteriaBetaproteobacteria Burkholderiales Oxalobacteraceae Janthinobacteriumlividum OTU_35 79 Proteobacteria Betaproteobacteria BurkholderialesComamonadaceae Polaromonas OTU_1226 80 Proteobacteria BetaproteobacteriaBurkholderiales Comamonadaceae OTU_1068 81 ProteobacteriaBetaproteobacteria Burkholderiales Oxalobacteraceae OTU_1252 82Proteobacteria Betaproteobacteria Burkholderiales Comamonadaceae OTU_11383 Proteobacteria Betaproteobacteria Burkholderiales OxalobacteraceaeJanthinobacterium OTU_39 84 Proteobacteria BetaproteobacteriaBurkholderiales Comamonadaceae OTU_345 85 ProteobacteriaBetaproteobacteria Burkholderiales Oxalobacteraceae Ralstonia OTU_168 86Proteobacteria Betaproteobacteria Burkholderiales Comamonadaceae OTU_787 Proteobacteria Betaproteobacteria Burkholderiales OxalobacteraceaeJanthinobacterium OTU_1344 88 Proteobacteria BetaproteobacteriaBurkholderiales Oxalobacteraceae OTU_87 89 Firmicutes ClostridiaClostridiales Clostridiaceae Clostridium butyricum OTU_206 90 FirmicutesClostridia Clostridiales Clostridiaceae Clostridium intestinale OTU_25891 Firmicutes Clostridia Clostridiales Clostridiaceae OTU_342 92Firmicutes Clostridia Clostridiales Clostridiaceae Thermoanaerobacteriumsaccharolyticum OTU_259 93 Firmicutes Clostridia Thermo-Caldicellulosiruptoraceae Caldicellulosiruptor saccharolyticusanaerobacterales OTU_428 94 Firmicutes Clostridia Thermo-Carboxydocellaceae Carboxydocella anaerobacterales OTU_485 95Bacteroidetes Cytophagia Cytophagales Cytophagaceae HymenobacterOTU_1306 96 Bacteroidetes Cytophagia Cytophagales CytophagaceaeHymenobacter OTU_735 97 Bacteroidetes Cytophagia CytophagalesCytophagaceae Hymenobacter OTU_37 98 Bacteroidetes CytophagiaCytophagales Cytophagaceae Hymenobacter OTU_775 99 BacteroidetesCytophagia Cytophagales Cytophagaceae Hymenobacter OTU_141 100Bacteroidetes Cytophagia Cytophagales Cytophagaceae Hymenobacter OTU_149101 Proteobacteria Deltaproteobacteria Myxococcales CystobacterineaeOTU_70 102 Bacteroidetes Flavobacteriia Flavobacteriales [Weeksellaceae]Chryseobacterium OTU_23 103 Bacteroidetes FlavobacteriiaFlavobacteriales [Weeksellaceae] Chryseobacterium OTU_236 104Bacteroidetes Flavobacteriia Flavobacteriales [Weeksellaceae]Chryseobacterium OTU_148 105 Bacteroidetes FlavobacteriiaFlavobacteriales [Weeksellaceae] Chryseobacterium OTU_181 106Bacteroidetes Flavobacteriia Flavobacteriales [Weeksellaceae]Chryseobacterium OTU_347 107 Proteobacteria GammaproteobacteriaEnterobacteriales Enterobacteriaceae OTU_1190 108 ProteobacteriaGammaproteobacteria Enterobacteriales Enterobacteriaceae YersiniaOTU_1201 109 Proteobacteria Gammaproteobacteria EnterobacterialesEnterobacteriaceae Enterobacter hormaechei OTU_679 110 ProteobacteriaGammaproteobacteria Pseudomonadales Pseudomonadaceae Pseudomonas fragiOTU_234 111 Proteobacteria Gammaproteobacteria PseudomonadalesPseudomonadaceae OTU_46 112 Proteobacteria GammaproteobacteriaPseudomonadales Moraxellaceae Acinetobacter lwoffii OTU_1274 113Proteobacteria Gammaproteobacteria Xanthomonadales XanthomonadaceaeStenotrophomonas maltophilia OTU_1303 114 ProteobacteriaGammaproteobacteria Enterobacteriales Enterobacteriaceae OTU_401 115Proteobacteria Gammaproteobacteria Enterobacteriales EnterobacteriaceaeOTU_1261 116 Proteobacteria Gammaproteobacteria EnterobacterialesEnterobacteriaceae OTU_548 117 Proteobacteria GammaproteobacteriaXanthomonadales Xanthomonadaceae Stenotrophomonas OTU_132 118Proteobacteria Gammaproteobacteria Pseudomonadales PseudomonadaceaePseudomonas veronii OTU_1343 119 Proteobacteria GammaproteobacteriaPseudomonadales Pseudomonadaceae OTU_22 120 ProteobacteriaGammaproteobacteria Pseudomonadales Pseudomonadaceae OTU_163 121Proteobacteria Gammaproteobacteria Xanthomonadales XanthomonadaceaeStenotrophomonas OTU_771 122 Proteobacteria GammaproteobacteriaPseudomonadales Pseudomonadaceae Pseudomonas OTU_826 123 ProteobacteriaGammaproteobacteria Pseudomonadales Pseudomonadaceae Pseudomonas OTU_166124 Proteobacteria Gammaproteobacteria Xanthomonadales XanthomonadaceaeXanthomonas OTU_1441 125 Proteobacteria GammaproteobacteriaEnterobacteriales Enterobacteriaceae OTU_1158 126 ProteobacteriaGammaproteobacteria Enterobacteriales Enterobacteriaceae Serratiamarcescens OTU_1083 127 Proteobacteria GammaproteobacteriaPseudomonadales Pseudomonadaceae OTU_8 128 ProteobacteriaGammaproteobacteria Pseudomonadales Pseudomonadaceae OTU_18 129Proteobacteria Gammaproteobacteria Xanthomonadales XanthomonadaceaeXanthomonas axonopodis OTU_51 130 Proteobacteria GammaproteobacteriaOceanospirillales Halomonadaceae Halomonas OTU_72 131 ProteobacteriaGammaproteobacteria Pseudomonadales Pseudomonadaceae Pseudomonasviridiflava OTU_9 132 Proteobacteria Gammaproteobacteria PseudomonadalesPseudomonadaceae Pseudomonas OTU_696 133 ProteobacteriaGammaproteobacteria Enterobacteriales Enterobacteriaceae Escherichiacoli OTU_53 134 Proteobacteria Gammaproteobacteria EnterobacterialesEnterobacteriaceae Enterobacter OTU_4 135 ProteobacteriaGammaproteobacteria Enterobacteriales Enterobacteriaceae Pantocaagglomerans OTU_220 136 Tenericutes Mollicutes AnaeroplasmatalesAnaeroplasmataceae Asteroleplasma OTU_343 137 BacteroidetesSphingobacteriia Sphingobacteriales Sphingobacteriaceae OTU_82 138Bacteroidetes Sphingobacteriia Sphingobacteriales SphingobacteriaceaePedobacter OTU_69 139 Bacteroidetes Sphingobacteriia SphingobacterialesSphingobacteriaceae OTU_36 140 Bacteroidetes SphingobacteriiaSphingobacteriales Sphingobacteriaceae Pedobacter OTU_1386 141Bacteroidetes Sphingobacteriia Sphingobacteriales SphingobacteriaceaePedobacter OTU_1165 142 Bacteroidetes SphingobacteriiaSphingobacteriales Sphingobacteriaceae Pedobacter cryoconitis OTU_368143 Bacteroidetes Sphingobacteriia SphingobacterialesSphingobacteriaceae Pedobacter OTU_91 144 Cyanobacteria

TABLE 4 Exemplary fungal endophytes present in all plants SEQ ID OTU_IDNO Phylum Class Order Family Genus Species OTU_288 145 BasidiomycotaAgaricomycetes Corticiales Corticiaceae Waitea circinata var circinataOTU_327 146 Basidiomycota Agaricomycetes CantharellalesCeratobasidiaceae Thanatephorus cucumeris OTU_1 147 AscomycotaDothideomycetes Pleosporales Pleosporaceae Alternaria sp MY 2011 OTU_2148 Ascomycota Dothideomycetes Capnodiales MycosphaerellaceaeCladosporium OTU_12 149 Ascomycota Dothideomycetes CapnodialesDavidiellaceae Davidiella tassiana OTU_9 150 Ascomycota DothideomycetesPleosporales Pleosporaceae Lewia infectoria OTU_29 151 AscomycotaDothideomycetes Pleosporales Pleosporaceae Epicoccum nigrum OTU_15 152Ascomycota Dothideomycetes Pleosporales Pleosporaceae Ulocladium OTU_55153 Ascomycota Dothideomycetes Capnodiales Davidiellaceae CladosporiumOTU_10 154 Ascomycota Dothideomycetes Pleosporales Incertae sedis Phomasp P48E5 OTU_133 155 Ascomycota Dothideomycetes CapnodialesDavidiellaceae Cladosporium sp ascomyc1 OTU_26 156 AscomycotaDothideomycetes Pleosporales Phaeosphaeriaceae unidentifiedPhaeosphaeriaceae sp MJ23 OTU_47 157 Ascomycota Dothideomycetes OTU_24158 Ascomycota Dothideomycetes Pleosporales Phaeosphaeriaceae OTU_522159 Ascomycota Dothideomycetes Pleosporales PhaeosphaeriaceaeAmpelomyces quisqualis OTU_66 160 Ascomycota DothideomycetesPleosporales Pleosporaceae Dendryphiella arenaria OTU_23 161 AscomycotaDothideomycetes Capnodiales Mycosphaerellaceae Septoria phalaridisOTU_71 162 Ascomycota Dothideomycetes Pleosporales OTU_27 163 AscomycotaDothideomycetes Pleosporales Incertae sedis OTU_32 164 AscomycotaDothideomycetes Dothideales Dothioraceae Aureobasidium OTU_20 165Ascomycota Dothideomycetes Pleosporales Phaeosphaeriaceae unidentifiedPhaeosphaeriaceae sp MJ23 OTU_16 166 Ascomycota DothideomycetesPleosporales Incertae sedis Phoma OTU_44 167 Ascomycota DothideomycetesCapnodiales Davidiellaceae Cladosporium sp 234B OTU_38 168 AscomycotaDothideomycetes Pleosporales Phaeosphaeriaceae OTU_104 169 AscomycotaDothideomycetes Pleosporales Pleosporaceae Alternaria brassicicolaOTU_1123 170 Ascomycota Dothideomycetes Pleosporales Phaeosphaeriaceaeunidentified Phaeosphaeriaceae sp MJ23 OTU_90 171 AscomycotaDothideomycetes Pleosporales Phaeosphaeriaceae Ampelomyces quisqualisOTU_48 172 Ascomycota Dothideomycetes Incertae sedis Incertae sedisLeptospora rubella OTU_73 173 Ascomycota Dothideomycetes PleosporalesIncertae sedis Phoma rhei OTU_1432 174 Ascomycota DothideomycetesPleosporales Leptosphaeriaceae unidentified uncultured EpicoccumOTU_1095 175 Ascomycota Dothideomycetes Pleosporales Pleosporaceae Lewiainfectoria OTU_486 176 Ascomycota Dothideomycetes PleosporalesPhaeosphaeriaceae Parastagonospora caricis OTU_110 177 AscomycotaDothideomycetes Capnodiales Davidiellaceae Cladosporium sp ascomyc1OTU_78 178 Ascomycota Dothideomycetes Pleosporales PhaeosphaeriaceaePhaeosphaeria OTU_83 179 Ascomycota Dothideomycetes unidentifiedunidentified unidentified Dothideomycetes sp OTU_815 180 AscomycotaDothideomycetes Pleosporales Pleosporaceae Alternaria sp MY_2011 OTU_244181 Ascomycota Dothideomycetes Capnodiales Davidiellaceae Cladosporiumsphaerospermum OTU_775 182 Ascomycota Dothideomycetes PleosporalesPleosporaceae Alternaria sp MY 2011 OTU_259 183 AscomycotaDothideomycetes Pleosporales Pleosporaceae Lewia infectoria OTU_447 184Ascomycota Dothideomycetes Pleosporales Incertae sedis Phoma macrostomaOTU_429 185 Ascomycota Dothideomycetes Pleosporales Incertae sedis Phomasp P48E5 OTU_122 186 Ascomycota Dothideomycetes Pleosporales Incertaesedis Phoma macrostoma OTU_82 187 Ascomycota DothideomycetesPleosporales Phaeosphaeriaceae unidentified Phaeosphaeriaceae sp OTU_324188 Ascomycota Dothideomycetes Pleosporales Pleosporaceae Lewiainfectoria OTU_60 189 Ascomycota Dothideomycetes PleosporalesPleosporaceae Cochliobolus OTU_142 190 Ascomycota DothideomycetesIncertae sedis Pseudeurotiaceae Pseudeurotium OTU_92 191 AscomycotaDothideomycetes Capnodiales Mycosphaerellaceae Cercospora nicotianaeOTU_87 192 Ascomycota Dothideomycetes Capnodiales MycosphaerellaceaeMycosphaerella punctiformis OTU_99 193 Ascomycota DothideomycetesPleosporales Leptosphaeriaceae OTU_1316 194 Ascomycota DothideomycetesPleosporales Incertae sedis Phoma OTU_138 195 Ascomycota DothideomycetesCapnodiales Davidiellaceae Cladosporium OTU_992 196 AscomycotaDothideomycetes Dothideales Dothioraceae Aureobasidium pullulans OTU_378197 Ascomycota Dothideomycetes Pleosporales Incertae sedis Phoma OTU_353198 Ascomycota Dothideomycetes Pleosporales Incertae sedis Phoma OTU_227199 Ascomycota Dothideomycetes Pleosporales Incertae sedis OTU_68 200Ascomycota Dothideomycetes Pleosporales Incertae sedis Phoma paspaliOTU_680 201 Ascomycota Dothideomycetes OTU_97 202 AscomycotaDothideomycetes Pleosporales Phaeosphaeriaceae unidentifiedPhaeosphaeriaceae sp MJ23 OTU_115 203 Ascomycota DothideomycetesPleosporales Phaeosphaeriaceae Phaeosphaeria OTU_22 204 AscomycotaEurotiomycetes Eurotiales Trichocomaceae Penicillium OTU_262 205Ascomycota Eurotiomycetes Eurotiales Trichocomaceae Penicillium citrinumOTU_17 206 Ascomycota Eurotiomycetes Eurotiales TrichocomaceaeAspergillus niger OTU_28 207 Ascomycota Eurotiomycetes EurotialesTrichocomaceae Penicillium bialowiezense OTU_21 208 AscomycotaEurotiomycetes Eurotiales Trichocomaceae unidentified unculturedEurotium OTU_938 209 Ascomycota Eurotiomycetes Eurotiales TrichocomaceaePenicillium OTU_64 210 Ascomycota Eurotiomycetes EurotialesTrichocomaceae Penicillium spinulosum OTU_105 211 AscomycotaEurotiomycetes Eurotiales Trichocomaceae Emericella nidulans OTU_527 212Ascomycota Eurotiomycetes Eurotiales Trichocomaceae Penicilliumbialowiezense OTU_121 213 Ascomycota Eurotiomycetes EurotialesTrichocomaceae Penicillium OTU_77 214 Ascomycota EurotiomycetesEurotiales Trichocomaceae Aspergillus flavus OTU_340 215 AscomycotaEurotiomycetes Eurotiales Trichocomaceae Penicillium OTU_186 216Ascomycota Eurotiomycetes Eurotiales Trichocomaceae Talaromyces OTU_131217 Ascomycota Eurotiomycetes Eurotiales Trichocomaceae Emericellanidulans OTU_18 218 Zygomycota Incertae sedis Mucorales RhizopodaceaeRhizopus oryzae OTU_6 219 Ascomycota Leotiomycetes HelotialesHelotiaceae OTU_42 220 Ascomycota Leotiomycetes Erysiphales ErysiphaceaeErysiphe cruciferarum OTU_125 221 Ascomycota Leotiomycetes HelotialesSclerotiniaceae Botrytis sp CID95 OTU_50 222 BasidiomycotaMicrobotryomycetes Sporidiobolales Incertae sedis Sporobolomycesoryzicola OTU_37 223 Basidiomycota Microbotryomycetes SporidiobolalesIncertae sedis Sporobolomyces roseus OTU_1406 224 BasidiomycotaMicrobotryomycetes Sporidiobolales Incertae sedis Sporobolomyces OTU_72225 Basidiomycota Microbotryomycetes Sporidiobolales Incertae sedisSporobolomyces ruberrimus OTU_1184 226 Basidiomycota MicrobotryomycetesSporidiobolales Incertae sedis Sporobolomyces roseus OTU_70 227Basidiomycota Microbotryomycetes Sporidiobolales Incertae sedisunidentified Sporidiobolales sp OTU_65 228 BasidiomycotaMicrobotryomycetes Sporidiobolales Incertae sedis Rhodosporidiumdiobovatum OTU_103 229 Basidiomycota Microbotryomycetes SporidiobolalesIncertae sedis Sporobolomyces symmetricus OTU_53 230 AscomycotaSaccharomycetes Saccharomycetales Pichiaceae Pichia fermentans OTU_94231 Ascomycota Saccharomycetes Saccharomycetales SaccharomycodaceaeHanseniaspora uvarum OTU_86 232 Ascomycota SaccharomycetesSaccharomycetales Saccharomycodaceae Hanseniaspora thailandica OTU_5 233Ascomycota Sordariomycetes Hypocreales Nectriaceae Fusarium OTU_11 234Ascomycota Sordariomycetes Xylariales Incertae sedis Monographella sp 68OTU_13 235 Ascomycota Sordariomycetes Hypocreales Nectriaceae Fusariumculmorum OTU_25 236 Ascomycota Sordariomycetes Sordariales OTU_120 237Ascomycota Sordariomycetes Hypocreales Incertae sedis Acremonium sp 2J12 OTU_1072 238 Ascomycota Sordariomycetes Hypocreales NectriaceaeGibberella intricans OTU_58 239 Ascomycota Sordariomycetes HypocrealesNectriaceae Gibberella intricans OTU_62 240 Ascomycota SordariomycetesHypocreales OTU_30 241 Ascomycota Sordariomycetes HypocrealesNectriaceae Gibberella baccata OTU_56 242 Ascomycota SordariomycetesHypocreales Incertae sedis Acremonium sp 4053 OTU_209 243 AscomycotaSordariomycetes Hypocreales Nectriaceae Fusarium petroliphilum OTU_34244 Ascomycota Sordariomycetes Incertae sedis PlectosphaerellaceaeGibellulopsis sp YH_2012 OTU_45 245 Ascomycota SordariomycetesXylariales Incertae sedis Monographella cucumerina OTU_100 246Ascomycota Sordariomycetes Hypocreales unidentified unidentified OTU_877247 Ascomycota Sordariomycetes Hypocreales Nectriaceae Fusariumsporotrichioides OTU_682 248 Ascomycota Sordariomycetes HypocrealesNectriaceae OTU_81 249 Ascomycota Sordariomycetes DiaporthalesDiaporthaceae Phomopsis sp MAFF 239532 OTU_238 250 AscomycotaSordariomycetes Sordariales Lasiosphaeriaceae unidentifiedLasiosphaeriaceae sp OTU_85 251 Ascomycota Sordariomycetes SordarialesChaetomiaceae Chaetomium globosum OTU_525 252 Ascomycota SordariomycetesOTU_106 253 Ascomycota Sordariomycetes Incertae sedis GlomerellaceaeColletotrichum acutatum OTU_150 254 Ascomycota SordariomycetesHypocreales Incertae sedis Acremonium dichromosporum OTU_1278 255Ascomycota Sordariomycetes Hypocreales Nectriaceae Fusariumsporotrichioides OTU_1403 256 Ascomycota Sordariomycetes XylarialesIncertae sedis Monographella sp 68 OTU_160 257 AscomycotaSordariomycetes Incertae sedis Plectosphaerellaceae Lectera longaOTU_1214 258 Ascomycota Sordariomycetes Hypocreales NectriaceaeGibberella intricans OTU_181 259 Ascomycota Sordariomycetes HypocrealesCordycipitaceae Engyodontium album OTU_172 260 AscomycotaSordariomycetes Hypocreales Nectriaceae Fusarium poae OTU_19 261Basidiomycota Tremellomycetes unidentified unidentified unidentifieduncultured Cryptococcus OTU_40 262 Basidiomycota TremellomycetesFilobasidiales Filobasidiaceae Cryptococcus OTU_74 263 BasidiomycotaTremellomycetes Tremellales Incertae sedis Cryptococcus victoriaeOTU_163 264 Basidiomycota Tremellomycetes Tremellales unidentifiedunidentified Tremellales sp TG05 OTU_52 265 BasidiomycotaTremellomycetes Tremellales Incertae sedis Cryptococcus victoriaeOTU_325 266 Basidiomycota Tremellomycetes Tremellales Incertae sedisHannaella OTU_128 267 Basidiomycota Tremellomycetes FilobasidialesFilobasidiaceae Cryptococcus wieringae OTU_180 268 BasidiomycotaTremellomycetes Tremellales Incertae sedis Cryptococcus laurentii OTU_46269 Basidiomycota Tremellomycetes Filobasidiales FilobasidiaceaeCryptococcus oeirensis OTU_174 270 Basidiomycota TremellomycetesTremellales Incertae sedis Cryptococcus sp VP_2009b OTU_69 271Basidiomycota Tremellomycetes Filobasidiales FilobasidiaceaeCryptococcus oeirensis OTU_80 272 Basidiomycota TremellomycetesCystofilobasidiales Cystofilobasidiaceae Udeniomyces puniceus OTU_96 273Basidiomycota Tremellomycetes Cystofilobasidiales CystofilobasidiaceaeUdeniomyces pyricola OTU_51 274 Basidiomycota TremellomycetesTremellales Incertae sedis Bullera Bullera unica OTU_109 275Basidiomycota Tremellomycetes Tremellales Incertae sedis Dioszegiafristingensis OTU_222 276 Basidiomycota TremellomycetesCystofilobasidiales Cystofilobasidiaceae Cystofilobasidiuminfirmominiatum OTU_1054 277 Basidiomycota TremellomycetesFilobasidiales Filobasidiaceae Cryptococcus oeirensis OTU_971 278Basidiomycota Tremellomycetes unidentified unidentified unidentifiedTremellomycetes sp OTU_79 279 Basidiomycota Tremellomycetes TremellalesIncertae sedis Hannaella luteola OTU_135 280 BasidiomycotaTremellomycetes Filobasidiales Filobasidiaceae Cryptococcus albidusOTU_166 281 Basidiomycota Tremellomycetes Tremellales Incertae sedisCryptococcus victoriae OTU_111 282 Basidiomycota Tremellomycetesunidentified unidentified unidentified Tremellomycetes sp OTU_158 283Basidiomycota Tremellomycetes unidentified unidentified unidentifiedTremellomycetes sp OTU_91 284 Basidiomycota TremellomycetesFilobasidiales Filobasidiaceae Cryptococcus albidus OTU_127 285Basidiomycota Tremellomycetes Tremellales Incertae sedis HannaellaOTU_1103 286 Basidiomycota Wallemiomycetes Wallemiales WallemiaceaeWallemia sebi OTU_54 287 Basidiomycota Wallemiomycetes WallemialesWallemiaceae Wallemia muriae OTU_114 288 Basidiomycota WallemiomycetesWallemiales Wallemiaceae Wallemia sebi OTU_1326 289 BasidiomycotaWallemiomycetes Wallemiales Wallemiaceae Wallemia muriae

TABLE 1 Exemplary core bacterial endophytes SEQ ID OTU_ID NO PhylumClass Order Family Genus Species OTU_47  39 AlphaproteobacteriaRhizobiales Methylobacteriaceae Methylobacterium OTU_14  43Alphaproteobacteria Sphingomonadales Sphingomonadaceae SphingomonasOTU_6  44 Alphaproteobacteria Sphingomonadales SphingomonadaceaeSphingomonas OTU_25  59 Bacilli Bacillales Paenibacillaceae OTU_19  64Bacilli Bacillales Paenibacillaceae Paenibacillus amylolyticus OTU_16 65 Bacilli Bacillales [Exiguobacteraceae] Exiguobacterium OTU_222  67Bacilli Bacillales Bacillaceae Geobacillus OTU_653  68 BacilliBacillales Bacillaceae Bacillus endophyticus OTU_11  69 BacilliBacillales Paenibacillaceae Paenibacillus OTU_71  70 Bacilli BacillalesPaenibacillaceae Saccharibacillus kuerlensis OTU_13  71 BacilliBacillales Bacillaceae Bacillus nexus OTU_1014  75 BetaproteobacteriaBurkholderiales Oxalobacteraceae Janthinobacterium OTU_168  86Betaproteobacteria Burkholderiales Comamonadaceae OTU_7  87Betaproteobacteria Burkholderiales Oxalobacteraceae JanthinobacteriumOTU_1344  88 Betaproteobacteria Burkholderiales OxalobacteraceaeOTU_1303 114 Gammaproteobacteria Enterobacteriales EnterobacteriaceaeOTU_401 115 Gammaproteobacteria Enterobacteriales EnterobacteriaceaeOTU_1261 116 Gammaproteobacteria Enterobacteriales EnterobacteriaceaeOTU_771 122 Gammaproteobacteria Pseudomonadales PseudomonadaceaePseudomonas OTU_1441 125 Gammaproteobacteria EnterobacterialesEnterobacteriaceae OTU_1158 126 Gammaproteobacteria EnterobacterialesEnterobacteriaceae Serratia marcescens OTU_8 128 GammaproteobacteriaPseudomonadales Pseudomonadaceae OTU_18 129 GammaproteobacteriaXanthomonadales Xanthomonadaceae Xanthomonas axonopodis OTU_51 130Gammaproteobacteria Oceanospirillales Halomonadaceae Halomonas OTU_9 132Gammaproteobacteria Pseudomonadales Pseudomonadaceae Pseudomonas OTU_696133 Gammaproteobacteria Enterobacteriales Enterobacteriaceae Escherichiacoli OTU_53 134 Gammaproteobacteria Enterobacteriales EnterobacteriaceaeEnterobacter OTU_4 135 Gammaproteobacteria EnterobacterialesEnterobacteriaceae Pantoea agglomerans

TABLE 2 Exemplary core fungal endophytes SEQ ID OUT_ID NO Phylum ClassOrder Family Genus Species OTU_1 147 Dothideomycetes PleosporalesPleosporaceae Alternaria sp MY_2011 OTU_2 148 DothideomycetesCapnodiales Mycosphaerellaceae unidentified uncultured CladosporiumOTU_12 149 Dothideomycetes Capnodiales Davidiellaceae Davidiellatassiana OTU_9 150 Dothideomycetes Pleosporales Pleosporaceae Lewiainfectoria OTU_815 180 Dothideomycetes Pleosporales PleosporaceaeAlternaria sp MY_2011 OTU_775 182 Dothideomycetes PleosporalesPleosporaceae Alternaria sp MY_2011 OTU_22 204 Eurotiomycetes EurotialesTrichocomaceae Penicillium OTU_6 219 Leotiomycetes HelotialesHelotiaceae OTU_50 222 Microbotryomycetes Sporidiobolales Incertae sedisSporobolomyces oryzicola OTU_37 223 Microbotryomycetes SporidiobolalesIncertae sedis Sporobolomyces roseus OTU_1406 224 MicrobotryomycetesSporidiobolales Incertae sedis Sporobolomyces OTU_1184 226Microbotryomycetes Sporidiobolales Incertae sedis Sporobolomyces roseusOTU_5 233 Sordariomycetes Hypocreales Nectriaceae Fusarium OTU_1072 238Sordariomycetes Hypocreales Nectriaceae Gibberella intricans OTU_58 239Sordariomycetes Hypocreales Nectriaceae Gibberella intricans OTU_682 248Sordariomycetes Hypocreales Nectriaceae OTU_19 261 Tremellomycetesunidentified unidentified unidentified uncultured Cryptococcus OTU_40262 Tremellomycetes Filobasidiales Filobasidiaceae Cryptococcus OTU_52265 Tremellomycetes Tremellales Incertae sedis Cryptococcus victoriaeOTU_166 281 Tremellomycetes Tremellales Incertae sedis Cryptococcusvictoriae

Example 2—Identification and Characterization of Culturable Bacterialand Fungal Endophytes Belonging to Core OTUs

In order to better understand the role played by core seed-derivedendophytic microbes in improving the vigor, general health and stressresilience of agricultural plants, we initiated a systematic screen toisolate and characterize endophytic microbes from seeds and tissues ofcommercially significant agricultural plants.

Seeds from diverse types of cereals, fruits, vegetables, grasses,oilseed, and other seeds were acquired and screened for cultivatablemicrobes, as described below. Culturable microbes (i.e., SYM strains)belonging to the same OTUs as the core OTUs described in Table 1 andTable 2 were isolated and identified.

Isolation of Bacteria and Fungi from the Interior of Seeds

Isolation of fungi and bacteria (including endophytes) from the interiorof surface-sterilized seeds was performed using techniques known in theart. Surface sterilized seeds were ground, diluted in liquid media, andthe suspension used to inoculate solid media plates. These wereincubated under different conditions at room temperature.

Experiment Description

Approximately fifty surface-sterilized seeds were transferredaseptically to a sterile blender and ground. The ground seeds wereresuspended in 50 mL of sterile R2A broth, and incubated for 4h at roomtemperature. Ten 1 mL aliquots of the seed homogenates were collectedand centrifuged, their supernatants discarded and the pellets gentlyresuspended in 1 mL of sterile 0.05 phosphate buffer; 0.5 mL of 50%glycerol is added to each of five tubes. These were stored at −80 C forfurther characterization. The remaining aliquots were diluted down twicein hundred-fold dilutions to 10-4. 100 microliters of the 1, 10-2, and10-4 dilutions were used to inoculate three Petri dishes containing thefollowing media in order to isolate of bacteria and/or fungi:

Tryptic Soy agar

R2A agar

Potato dextrose agar

Sabouraud Agar

Other Media Depending on Target Microorganism

The plates were divided into three sets comprising each media type andincubated in different environments. The first set was incubatedaerobically, the second under anaerobic conditions, and the third undermicroaerophilic conditions and all were inspected daily for up to 5days. 1-2 individual colonies per morphotype were isolated and streakedfor purity onto fresh plates of the same media/environment from whichthe microorganism was isolated. Plates were incubated at roomtemperature for 2-5 days. After an isolate grew it was streaked oncemore onto a fresh plate of the same media to ensure purity and incubatedunder the same environmental conditions.

From the second streaked plate, isolates were stored in Tryptic soybroth+15% glycerol at −80° C. for further characterization, by firstscraping 2-3 colonies (about 10 μL) from the plate into a cryogenic tubecontaining 1.5 mL of the above-mentioned media and gently resuspendingthe cells. Alternatively, isolates were propagated in specialized mediaas recommended for the particular taxon of microorganism. The microbesobtained represent those that live in the seeds of the plant accession.

Isolation of Bacteria and Fungi from Plant Interior Tissues

Isolation of fungi and bacteria (including endophytes) fromsurface-sterilized plant tissues was performed using techniques known inthe art. Surface sterilized plant tissues were ground, diluted in liquidmedia, and then this suspension was used to inoculate solid mediaplates. These were incubated under different environmental conditions atroom temperature.

Experiment Description

Approximately fifty grams of surface-sterilized plant tissue weretransferred aseptically to a sterile blender and ground. The groundtissue was resuspended in 50 mL of sterile R2A broth, and incubated for4h at room temperature. Ten 1 mL aliquots of the plant tissuehomogenates were collected and centrifuged, their supernatants discardedand the pellets gently resuspended in 1 mL of sterile 0.05 phosphatebuffer. 0.5 mL of 50% Glycerol was added to each of five tubes. Thesewere stored at −80° C. for possible further characterization. Theremaining aliquots were diluted down twice in hundred-fold dilutions to10-4. One hundred microliters of the 1, 10-2, and 10-4 dilutions wereused to inoculate three Petri dishes containing the following media inorder to isolate of bacteria and/or fungi:

Tryptic Soy agar

R2A agar

Potato dextrose agar

Sabouraud Agar

Other Media Depending on Target Microorganism

Plates were divided into three sets comprising each media type andincubated in different environments. The first set was incubatedaerobically, the second under anaerobic conditions, and the third undermicroaerophilic conditions and all were inspected daily for up to 5days. 1-2 individual colonies per morphotype were isolated and streakedfor purity onto fresh plates of the same media/environment from whichthe microorganism was isolated. Plates were incubated at roomtemperature for 2-5 days. After an isolate grew it was streaked oncemore onto a fresh plate of the same media to ensure purity and incubatedunder the same environmental conditions.

From the second streaked plate, isolates were stored in Tryptic soybroth+15% glycerol at −80° C. for further characterization, by firstscraping 2-3 colonies (about 10 μL) from the plate into a cryogenic tubecontaining 1.5 mL of the above-mentioned media and gently resuspendingthe cells. Alternatively, isolates were propagated in specialized mediaas recommended for the particular taxon of microorganism.

Isolation of Bacteria and Fungi from Plant or Seed Surfaces

To collect phyllosphere, rhizosphere, or spermosphere material forculturing of microbes, unwashed shoot, roots or seeds were shakenfree/cleaned of any attached soil and stuffed into sterile 50 mL Falcontubes. To these, 10 mL of sterile 0.1 M sodium phosphate buffer wasadded and shaken, followed by 5 minutes of sonication to dislodgemicrobes from plant surfaces, with the resulting cloudy or muddy washcollected in a separate 15 mL Falcon tube. 100 μL of this microbe filledwash was directly spread onto agar plates or nutrient broth forculturing and enrichment, or it was further diluted with sterile 0.1 Msodium phosphate buffer by 10×, 100×, 1,000×, 10,000× and even 100,000×,before microbial culturing on agar plates or nutrient broth. Glycerolstock preparations of the plant surface wash solution were made at thispoint by mixing 1 mL of the soil wash solution and 0.5 mL of sterile,80% glycerol, flash freezing the preparation in a cryotube dipped inliquid nitrogen, and storing at −80° C. Nutrient broth inoculated with amixture of plant surface bacteria forms a stable, mixed community ofmicrobes which was used in plant inoculation experiments describedherein, subcultured in subsequent broth incubations, or spread on agarplates and separated into individual colonies which were tested viamethods described herein.

Characterization of Fungal and Bacterial Isolates

Characterization of fungi and bacteria isolated from surface-sterilizedor non-sterilized plant or seed tissues was performed using techniquesknown in the art. These techniques take advantage of differentialstaining of microorganisms, morphological characteristics of cells,spores, or colonies, biochemical reactions that provide differentialcharacterization, and DNA amplification and sequencing of diagnosticregions of genes, among other methods.

Experimental Description

Isolates of bacteria and/or fungi isolated as described herein(including endophytic bacteria and fungi) were categorized into threetypes: bacterial isolates, fungal isolates, and unknown isolates (sinceyeast colonies can resemble bacterial colonies in some cases) based oncolony morphology, formation of visible mycelia, and/or formation ofspores. To determine if an unknown isolate was bacterial or fungal,microscopic analysis of the isolates was performed. Some of the analysesknown to the art to differentiate microorganisms include, but are notlimited to: the 10% KOH test, positive staining with Lactophenol cottonblue, Gram staining, and growth on media with selective agents. Thedistinguishing features observed by these tests are relative cell size(yeast size is much larger than bacterial size), formation of hyphae andspores (filamentous bacteria form smaller hyphae than fungi, and do notform structures containing spores), or growth under selection agents(most bacteria can grow in the presence of antifungal compounds likenystatin, while most fungi cannot; likewise, most fungi are unaffectedby the presence of broad-spectrum antibiotics like chloramphenicol andspectinomycin).

To identify the isolates, DNA sequence analysis of conserved genomicregions like the ribosomal DNA loci was performed. To obtain DNA toperform PCR amplifications, some cellular growth from solid media(approximately 5-10 μL) was resuspended in 30 μL of sterile Tris/EDTAbuffer (pH 8.0). Samples were heated to 98° C. for 10 minutes followedby cooling down to 4° C. for 1 minute in a thermocycler. This cycle wasrepeated twice. Samples were then centrifuged at ˜13,000 RCF for 1-5minutes and used as DNA template for PCR reactions. Below is a series ofexemplary primer combinations used to identify isolates to a genuslevel.

TABLE 5Exemplary primer combinations for isolate identification at a genus levelPrimer 1 Primer 2 Target V4_515F (5′ - V4_806R (5′-The 4th Variable region of GTGCCAGCMGCCGCGGTAA- GGACTACHVGGGTWTCTAAT-3′)the bacterial 16S rDNA 3′)(SEQ ID NO: 453) (SEQ ID NO: 454) 27F (5′-1492R (5′- Full length of the bacterial AGAGTTTGATCCTGGCTCAG-GGTTACCTTGTTACGACTT-3′) 16S rDNA, from position 8- 3′)(SEQ ID NO: 455)(SEQ ID NO: 456) 1507. ITS1 (5′- ITS2 (5′ - ~240 bp ITS1 region ofTCCGTAGGTGAACCTGCGG- GCTGCGTTCTTCATCGATGC- 3′) fungal genome3′)(SEQ ID NO: 457) (SEQ ID NO: 458) SR1R (5′ -SR6 (5′ -TGTTACGACTTTTACTT- Small subunit (18s) of theTACCTGGTTGATQCTGCCAGT- 3′)(SEQ ID NO: 460) fungal rDNA gene3′)(SEQ ID NO: 459) ITS1F (5′- ITS4 (5′- ~600-1000 bp ITS region ofCTTGGTCATTTAGAGGAAGTA TCCTCCGCTTATTGATATGC-3′) fungal genomesA-3′)(SEQ ID NO: 461) (SEQ ID NO: 462) ITS5 (Universal)(5′-ITS4Asco (Ascomycota-specific): ~500 bp fragment fromGGAAGTAAAAGTCGTAACAA 5′ different fungal Phyla GG-3′)(SEQ ID NO: 463)CGTTACTRRGGCAATCCCTGTTG 3′ (SEQ ID NO: 464) orITS4Basidio (Basidiomycota- specific): 5′ GCRCGGAARACGCTTCTC3′(SEQ ID NO: 465); or ITS4Chytrid (Chytridiomycota- specific): 5′TTTTCCCGTTTCATTCGCCA 3′ (SEQ ID NO: 466); orITS4Oo (Oomycota-specific): 5′ ATAGACTACAATTCGCC 3′ (SEQ ID NO: 467); orITS4Zygo (Zygomycota-specific): 5′ AAAACGTWTCTTCAAA 3′ (SEQ ID NO: 468).SSUmAf - (equimolar mix of 2 LSUmAr (equimolar mix of 41000-1600 bp fragment of degenerate primers) anddegenerate primers) and LSUmBr the Glomerycota (arbuscularSSUmCf equimolar mix of 3 (equimolar mix of 5 degeneratemycorrhizae) genome degenerate primers) primers) comprising partial SSU,whole internal transcribed spacer (ITS) rDNA region and partial LSU.Arch 340F (5′- Arch 1000R (5′- ~660 bp product of the 18SCCCTAYGGGGYGCASCAG-3′) GAGARGWRGTGCATGGCC-3′) from Archaea(SEQ ID NO: 469) (SEQ ID NO: 470) 27F-Degen (5′- 27F-Degen (5′-Full length of the bacterial AGRRTTYGATYMTGGYTYAG-HGGHTACCTTGTTACGACTT-3′) 16S rDNA, from position 8- 3′)(SEQ ID NO: 471)(SEQ ID NO: 472) 1507. and 799f (5′- AACMGGATTAGATACCCKG-3′)(SEQ ID NO: 473)

To decrease background noise due to the non-specific binding of primersto DNA, the thermocycler was programmed for a touchdown-PCR, whichincreased specificity of the reaction at higher temperatures andincreased the efficiency towards the end by lowering the annealingtemperature. Exemplary conditions for performing Touchdown PCR are shownin Table 6.

TABLE 6 Exemplary conditions for performing Touchdown PCR Step # CycleTemperature Time 1 Initial 98° C.* 5 m Denaturalization 2Denaturalization 98° C.* 30 s 3 Annealing Predicted optimal Tm for the30 s primer set +10° C., minus 1° C./cycle 4 Elongation 72° C.* 1 m/1Kb5 GoTo Step 2 × 10 times 6 Denaturalization 98° C.* 30 s 7 AnnealingPredicted optimal Tm for the 30 s primer set 8 Elongation 72° C.* 1m/1Kb 9 GoTo Step 6 × 20 times 10 Final Elongation 72° C.* 5 m 11 CoolDown 4° C. 5 m *Or the temperature specified by the DNA polymerasemanufacturer for this step.

PCR reactions were purified to remove primers, dNTPs, and othercomponents by methods known in the art, for example by the use ofcommercially available PCR clean-up kits.

The resulting sequences were aligned as query sequences with thepublicly available databases GenBank nucleotide, RDP, UNITE and PlutoF.RDP was specifically compiled and used for bacterial 16s classification.UNITE and PlutoF were specifically compiled and used for identificationof fungi. In all the cases, the strains were identified to species levelif their sequences were more than 95% similar to any identifiedaccession from all databases analyzed. When the similarity percentagewas between 90-97%, the strain was classified at genus, family, order,class, subdivision or phylum level depending on the informationdisplayed in databases used. Isolates with lower similarity values (from30-90%) were classified as “unknown” or “uncultured” depending on theinformation displayed after BLAST analysis. To compliment the molecularidentification, fungal taxa were confirmed by inducing sporulation onPDA or V8 agar plates and using reported morphological criteria foridentification of fruiting bodies structure and shape. Bacterial taxawere confirmed by using reported morphological criteria in specializeddifferential media for the particular taxon, or by biochemicaldifferentiation tests, as described by the Bergey's Manual of SystematicMicrobiology (Whitman, William B., et al., eds. Bergey's Manual® ofsystematic bacteriology. Vols. 1-5. Springer, 2012).

Culture-Independent Characterization of Fungal and Bacterial Communitiesin Seeds or Plants

To understand the diversity of culturable and unculturable microbial(e.g., bacterial and fungal) taxa that reside inside of seeds or plantsof agriculturally-relevant cultivars, landraces, and ancestral wildvarieties, microbial DNA was extracted from surface sterilized seed orplant parts, as described herein, followed by amplification of conservedgenomic regions, for example the ribosomal DNA loci. Amplified DNArepresented a “snapshot” of the full microbial community inside seeds orplants.

Experimental Description

To obtain microbial DNA from seeds, plants or plant parts, the seeds,plants or plant parts were surface sterilized under aseptic conditionsas described herein. Microbial DNA from seeds, plants, or plant partswas extracted using methods known in the art, for example usingcommercially available Seed-DNA or plant DNA extraction kits, or thefollowing method.

A sample of each kind of seed or plant tissue is placed in acold-resistant container and 10-50 mL of liquid nitrogen is applied. Theseeds or plant tissues are then macerated to a powder.

Genomic DNA is extracted from each seed or plant tissue preparation,following a chloroform:isoamyl alcohol 24:1 protocol (Sambrook et al.1989).

Fungal-specific primers were used to amplify the ITS (InternalTranscribed Spacer) region of nuclear ribosomal DNA. Bacterial specificprimers were used to amplify region of the 16s rDNA gene of thebacterial genome. Sequences obtained through NGS platforms were analyzedagainst databases, such as the ones mentioned herein.

Exemplary primer pairs used for this analysis are listed in Table 5.

As an alternative to next generation sequencing, Terminal RestricitionFragment Length Polymorphism, (TRFLP) can be performed. Group specific,fluorescently labeled primers are used to amplify diagnostic regions ofgenes in the microbial population. This fluorescently labeled PCRproduct is cut by a restriction enzyme chosen for heterogeneousdistribution in the PCR product population. The enzyme cut mixture offluorescently labeled and unlabeled DNA fragments is then submitted forsequence analysis on a Sanger sequence platform such as the AppliedBiosystems 3730 DNA Analyzer.

Determination of the Plant Pathogenic Potential of Microbial Isolates

Since a microbe that confers positive traits to one cultivar might be apathogenic agent in a different plant species, a general assay was usedto determine the pathogenic potential of microbial isolates. Surface andinterior-sterilized seeds are germinated in water agar, and once theplant develops its first set of leaves, are inoculated with the isolate.Alternatively, the plants are inoculated as seeds. For inoculation themicrobial isolate is grown on solid media, and inoculated into a plantor onto a seed via any of the methods described herein. Plants areallowed to grow under ideal conditions for 2-3 weeks and any pathogeniceffect of the introduced microbe is evaluated against uninoculatedcontrol plants.

Identification of Culturable Microbial Isolates that Correspond to CoreOTUs

To accurately characterize the isolated microbial endophytes, colonieswere submitted for marker gene sequencing, and the sequences wereanalyzed to provide taxonomic classifications. Among the culturedmicrobes (SYM strains), those with at least 97% 16S or ITS sequencesimilarity to OTUs of Table 1 and Table 2 were identified. Exemplaryisolated microbes that correspond to core OTUs are listed in Table 7(bacteria) and Table 8 (fungi).

TABLE 7 Exemplary bacterial endophytes SEQ ID NO SYM TaxonomicClassification 290 SYM00003 Bacteria; Proteobacteria;Betaproteobacteria; Burkholderiales; Oxalobacteraceae; Ralstoniapickettii 291 SYM00009 Bacteria; Proteobacteria; Betaproteobacteria;Burkholderiales; Oxalobacteraceae; Ralstonia pickettii 292 SYM00013Bacteria; Proteobacteria; Gammaproteobacteria; Pseudomonadales;Pseudomonadaceae; Pseudomonas oryzihabitans 293 SYM00017A Bacteria;Proteobacteria; Alphaproteobacteria; Rhizobiales; Rhizobiaceae;Agrobacterium larrymoorei 294 SYM00018 Bacteria; Proteobacteria;Gammaproteobacteria; Enterobacteriales; Enterobacteriaceae; Pantoeadispersa 295 SYM00020 Bacteria; Proteobacteria; Gammaproteobacteria;Enterobacteriales; Enterobacteriaceae; Pantoea dispersa 296 SYM00021bBacteria; Proteobacteria; Gammaproteobacteria; Enterobacteriales;Enterobacteriaceae; Escherichia hermannii 297 SYM00025 Bacteria;Proteobacteria; Gammaproteobacteria; Enterobacteriales;Enterobacteriaceae; Pantoea dispersa 298 SYM00033 Bacteria;Proteobacteria; Gammaproteobacteria; Enterobacteriales;Enterobacteriaceae; Enterobacter ludwigii 300 SYM00043 Bacteria;Proteobacteria; Gammaproteobacteria; Enterobacteriales;Enterobacteriaceae; Pantoea dispersa 301 SYM00044 Bacteria;Proteobacteria; Gammaproteobacteria; Enterobacteriales;Enterobacteriaceae; Enterobacter hormaechei 302 SYM00050 Bacteria;Proteobacteria; Gammaproteobacteria; Enterobacteriales;Enterobacteriaceae; Enterobacter cloacae 303 SYM00053 Bacteria;Proteobacteria; Gammaproteobacteria; Enterobacteriales;Enterobacteriaceae; Escherichia hermannii 305 SYM00062c Bacteria;Firmicutes; Bacilli; Bacillales; Paenibacillaceae; Saccharibacilluskuerlensis 306 SYM00065 Bacteria; Proteobacteria; Alphaproteobacteria;Sphingomonadales; Sphingomonadaceae; Sphingomonas sanguinis 308 SYM00068Bacteria; Proteobacteria; Gammaproteobacteria; Pseudomonadales;Pseudomonadaceae; Pseudomonas psychrotolerans 309 SYM00070 Bacteria;Proteobacteria; Gammaproteobacteria; Enterobacteriales;Enterobacteriaceae; Pantoea agglomerans 310 SYM00074 Bacteria;Proteobacteria; Gammaproteobacteria; Enterobacteriales;Enterobacteriaceae; Enterobacter cloacae 311 SYM00103 Bacteria;Proteobacteria; Betaproteobacteria; Burkholderiales; Oxalobacteraceae;Ralstonia pickettii 321 SYM00170 Bacteria; Firmicutes; Bacilli;Bacillales; Paenibacillaceae; Paenibacillus hunanensis 322 SYM00183Bacteria; Proteobacteria; Gammaproteobacteria; Xanthomonadales;Xanthomonadaceae; Stenotrophomonas maltophilia 323 SYM00184 Bacteria;Proteobacteria; Gammaproteobacteria; Xanthomonadales; Xanthomonadaceae;Stenotrophomonas maltophilia 324 SYM00207 Bacteria; Firmicutes; Bacilli;Bacillales; Bacillaceae; Bacillus pumilus 325 SYM00212 Bacteria;Firmicutes; Bacilli; Bacillales; Bacillaceae; Bacillus sp. 326 SYM00219Bacteria; Firmicutes; Bacilli; Bacillales; Bacillaceae; Bacillus sp. 327SYM00234 Bacteria; Firmicutes; Bacilli; Bacillales; Paenibacillaceae;Paenibacillus sp. 328 SYM00236 Bacteria; Proteobacteria;Alphaproteobacteria; Rhizobiales; Methylobacteriaceae; Methylobacteriumsp. 329 SYM00248 Bacteria; Proteobacteria; Gammaproteobacteria;Enterobacteriales; Enterobacteriaceae; Pantoea sp. 330 SYM00249Bacteria; Firmicutes; Bacilli; Bacillales; Bacillaceae; Bacillus sp. 331SYM00506C Bacteria; Firmicutes; Bacilli; Bacillales; Paenibacillaceae;Paenibacillus sp. 332 SYM00507 Bacteria; Firmicutes; Bacilli;Bacillales; Bacillaceae; Bacillus sp. 333 SYM00508 Bacteria;Proteobacteria; Gammaproteobacteria; Enterobacteriales;Enterobacteriaceae; Enterobacter asburiae 334 SYM00525 Bacteria;Actinobacteria; incertae sedis; Actinomycetales; Microbacteriaceae;Curtobacterium sp. 335 SYM00538A Bacteria; Proteobacteria;Alphaproteobacteria; Sphingomonadales; Sphingomonadaceae; Sphingomonasaquatilis 336 SYM00538B Bacteria; Firmicutes; Bacilli; Bacillales;Paenibacillaceae; Paenibacillus sp. 337 SYM00538i Bacteria;Bacteroidetes; Flavobacteriia; Flavobacteriales; [Weeksellaceae];Chryseobacterium sp. 338 SYM00543 Bacteria; Firmicutes; Bacilli;Bacillales; Bacillaceae; Bacillus sp. 339 SYM00545 Bacteria; Firmicutes;Bacilli; Bacillales; Paenibacillaceae; Paenibacillus sp. 340 SYM00549Bacteria; Firmicutes; Bacilli; Bacillales; Paenibacillaceae;Paenibacillus sp. 341 SYM00563 Bacteria; Firmicutes; Bacilli;Bacillales; Bacillaceae; Bacillus sp. 343 SYM00574 Bacteria;Proteobacteria; Betaproteobacteria; Burkholderiales; Burkholderiaceae;Burkholderia gladioli 347 SYM00617 Bacteria; Firmicutes; Bacilli;Bacillales; Bacillaceae; Bacillus sp. 348 SYM00620 Bacteria;Proteobacteria; Gammaproteobacteria; Enterobacteriales;Enterobacteriaceae; Enterobacter sp. 350 SYM00627 Bacteria;Proteobacteria; Gammaproteobacteria; Enterobacteriales;Enterobacteriaceae; Enterobacter sp. 351 SYM00628 Bacteria;Proteobacteria; Gammaproteobacteria; Enterobacteriales;Enterobacteriaceae; Enterobacter sp. 353 SYM00646 Bacteria;Proteobacteria; Gammaproteobacteria; Pseudomonadales; Pseudomonadaceae;Pseudomonas sp. 354 SYM00650 Bacteria; Proteobacteria;Gammaproteobacteria; Pseudomonadales; Pseudomonadaceae; Pseudomonas sp.355 SYM00662 Bacteria; Proteobacteria; Gammaproteobacteria;Pseudomonadales; Pseudomonadaceae; Pseudomonas putida 358 SYM00714Bacteria; Proteobacteria; Alphaproteobacteria; Rhizobiales;Rhizobiaceae; Agrobacterium sp. 365 SYM00905 Bacteria; Proteobacteria;Gammaproteobacteria; Xanthomonadales; Xanthomonadaceae; Stenotrophomonassp. 366 SYM00924 Bacteria; Proteobacteria; Alphaproteobacteria;Rhizobiales; Methylobacteriaceae; Methylobacterium sp. 367 SYM00963Bacteria; Proteobacteria; Gammaproteobacteria; Enterobacteriales;Enterobacteriaceae; Escherichia coli 368 SYM00982 Bacteria;Bacteroidetes; Flavobacteriia; Flavobacteriales; [Weeksellaceae];Chryseobacterium sp. 369 SYM00987 Bacteria; Proteobacteria;Gammaproteobacteria; Enterobacteriales; Enterobacteriaceae; Escherichiacoli 370 SYM00978 Bacteria; Proteobacteria; Alphaproteobacteria;Rhizobiales; Methylobacteriaceae; Methylobacterium aquaticum 371SYM00991 Bacteria; Proteobacteria; Beta Proteobacteria; Burkholderiales;Comamonadaceae; Acidovorax avenae 372 SYM00999 Bacteria; Proteobacteria;Alphaproteobacteria; Rhizobiales; Methylobacteriaceae; Methylobacteriumsp. 373 SYM01049 Bacteria; Proteobacteria; Gammaproteobacteria;Enterobacteriales; Enterobacteriaceae; Enterobacter sp. 426 SYM00057BBacteria; Proteobacteria; Betaproteobacteria; Burkholderiales;Burkholderiaceae; Burkholderia caledonica 427 SYM00091 Bacteria;Proteobacteria; Alphaproteobacteria; Rhizobiales; Rhizobiaceae;Rhizobium sp. 428 SYM00092D Bacteria; Proteobacteria;Alphaproteobacteria; Caulobacterales; Caulobacteraceae; Brevundimonassp. 430 SYM00290 Bacteria; Proteobacteria; Gammaproteobacteria;Pseudomonadales; Moraxellaceae; Acinetobacter Iwoffii 433 SYM00576Bacteria; Proteobacteria; Gammaproteobacteria; Enterobacteriales;Enterobacteriaceae; Pantoea dispersa 434 SYM00607 Bacteria;Proteobacteria; Gammaproteobacteria; Enterobacteriales;Enterobacteriaceae; Pantoea stewartii 435 SYM00619 Bacteria; Firmicutes;Bacilli; Bacillales; [Exiguobacteraceae]; Exiguobacterium acetylicum 436SYM00786 Bacteria; Proteobacteria; Gammaproteobacteria;Enterobacteriales; Enterobacteriaceae; Pantoea dispersa 437 SYM00879Bacteria; Proteobacteria; Alphaproteobacteria; Rhizobiales;Methylobacteriaceae; Methylobacterium populi 438 SYM00879B Bacteria;Proteobacteria; Alphaproteobacteria; Sphingomonadales;Sphingomonadaceae; Sphingomonas aquatilis 439 SYM00906 Bacteria;Proteobacteria; Gammaproteobacteria; Xanthomonadales; Xanthomonadaceae;Stenotrophomonas rhizophila 440 SYM00965 Bacteria; Proteobacteria;Alphaproteobacteria; Sphingomonadales; Erythrobacteraceae; Luteibacteryeojuensis 441 SYM01004 Bacteria; Proteobacteria; Alphaproteobacteria;Rhizobiales; Rhizobiaceae; Agrobacterium larrymoorei 442 SYM01022Bacteria; Actinobacteria; incertae sedis; Actinomycetales;Microbacteriaceae; Curtobacterium flaccumfaciens; 451 SYM00865 Bacteria;Proteobacteria; Gammaproteobacteria; Xanthomonadales; Xanthomonadaceae;Stenotrophomonas rhizophila 452 SYM01158 Bacteria; Proteobacteria;Gammaproteobacteria; Enterobacteriales; Enterobacteriaceae; Pantoeaagglomerans

TABLE 8 Exemplary fungal endophytes SEQ ID NO SYM TaxonomicClassification 299 SYM00034 Fungi; Ascomycota; Sordariomycetes;Hypocreales; Incertae sedis; Acremonium zeae 304 SYM00061A Fungi;Ascomycota; Sordariomycetes; Hypocreales; Incertae sedis; Acremoniumzeae 307 SYM00066 Fungi; Ascomycota; Sordariomycetes; Hypocreales;Incertae sedis; Acremonium zeae 312 SYM00120 Fungi; Ascomycota;Dothideomycetes; Pleosporales; Pleosporaceae; Alternaria alternata 313SYM00122 Fungi; Ascomycota; Dothideomycetes; Pleosporales;Pleosporaceae; Epicoccum nigrum 314 SYM00123 Fungi; Ascomycota;Dothideomycetes; Pleosporales; Pleosporaceae; Epicoccum nigrum 315SYM00124 Fungi; Ascomycota; Sordariomycetes; Hypocreales; Nectriaceae;Fusarium graminearum 316 SYM00129 Fungi; Ascomycota; Sordariomycetes;Hypocreales; Nectriaceae; Fusarium proliferatum 317 SYM00135 Fungi;Ascomycota; Sordariomycetes; Hypocreales; Nectriaceae; Fusariumproliferatum 318 SYM00136 Fungi; Ascomycota; Sordariomycetes;Hypocreales; Nectriaceae; Fusarium proliferatum 319 SYM00151 Fungi;Ascomycota; Sordariomycetes; Hypocreales; Nectriaceae; Fusariumproliferatum 320 SYM00154 Fungi; Ascomycota; Sordariomycetes;Hypocreales; Nectriaceae; Fusarium sp. 342 SYM00566B Fungi; Ascomycota;Sordariomycetes; Hypocreales; Incertae sedis; Acremonium zeae 344SYM00577 Fungi; Ascomycota; Sordariomycetes; Hypocreales; Incertaesedis; Acremonium zeae 345 SYM00590 Fungi; Ascomycota; Sordariomycetes;Hypocreales; Incertae sedis; Acremonium zeae 346 SYM00603 Fungi;Ascomycota; Sordariomycetes; Hypocreales; Incertae sedis; Acremoniumzeae 349 SYM00622 Fungi; Ascomycota; Sordariomycetes; Hypocreales;Incertae sedis; Acremonium strictum 352 SYM00629 Fungi; Ascomycota;Sordariomycetes; Hypocreales; Incertae sedis; Acremonium strictum 356SYM00663 Fungi; Ascomycota; Dothideomycetes; Pleosporales;Pleosporaceae; Alternaria alternata 357 SYM00696 Fungi; Ascomycota;Dothideomycetes; Pleosporales; Pleosporaceae; Alternaria tenuissima 359SYM00741a Fungi; Ascomycota; Dothideomycetes; Pleosporales; Incertaesedis; Phoma herbarum 360 SYM00741b Fungi; Ascomycota; Dothideomycetes;Capnodiales; Davidiellaceae; Cladosporium tenuissimum 361 SYM00793Fungi; Ascomycota; Sordariomycetes; Hypocreales; Nectriaceae; Fusariumverticillioides 362 SYM00795 Fungi; Ascomycota; Sordariomycetes;Hypocreales; Incertae sedis; Acremonium zeae 363 SYM00854 Fungi;Ascomycota; Dothideomycetes; Pleosporales; Pleosporaceae; Epicoccumsorghinum 364 SYM00880 Fungi; Ascomycota; Dothideomycetes; Pleosporales;Pleosporaceae; Alternaria tenuissima 374 SYM01300 Fungi; Ascomycota;Sordariomycetes; Hypocreales; Incertae sedis; Acremonium zeae 375SYM01303 Fungi; Ascomycota; Sordariomycetes; Hypocreales; Nectriaceae;Fusarium sp. 376 SYM01310 Fungi; Ascomycota; Sordariomycetes;Hypocreales; Nectriaceae; Fusarium proliferatum 377 SYM01311 Fungi;Ascomycota; Sordariomycetes; Hypocreales; Nectriaceae; Fusarium sp. 378SYM01314 Fungi; Ascomycota; Sordariomycetes; Hypocreales; Incertaesedis; Acremonium zeae 379 SYM01315 Fungi; Ascomycota; Dothideomycetes;Capnodiales; Davidiellaceae; Cladosporium sp. 380 SYM01325 Fungi;Ascomycota; Dothideomycetes; Pleosporales; Pleosporaceae; Alternaria sp.381 SYM01326 Fungi; Ascomycota; Dothideomycetes; Pleosporales;Pleosporaceae; Alternaria alternata 382 SYM01327 Fungi; Ascomycota;Dothideomycetes; Capnodiales; Davidiellaceae; Cladosporium sp. 383SYM01328 Fungi; Ascomycota; Dothideomycetes; Pleosporales;Pleosporaceae; Alternaria sp. 384 SYM01333 Fungi; Ascomycota;Dothideomycetes; Pleosporales; Pleosporaceae; Alternaria infectoria 385SYM15811 Fungi; Ascomycota; Dothideomycetes; Pleosporales;Pleosporaceae; Alternaria sp. 386 SYM15820 Fungi; Ascomycota;Sordariomycetes; Trichosphaeriales; incertae sedis; Nigrospora oryzae387 SYM15821 Fungi; Ascomycota; Sordariomycetes; Trichosphaeriales;incertae sedis; Nigrospora oryzae 388 SYM15825 Fungi; Ascomycota;Sordariomycetes; Hypocreales; Nectriaceae; Fusarium sp. 389 SYM15828Fungi; Ascomycota; Sordariomycetes; Hypocreales; Nectriaceae; Fusariumsp. 390 SYM15831 Fungi; Ascomycota; Sordariomycetes; Hypocreales;Nectriaceae; Fusarium sp. 391 SYM15837 Fungi; Ascomycota;Sordariomycetes; Hypocreales; Nectriaceae; Fusarium sp. 392 SYM15839Fungi; Ascomycota; Sordariomycetes; Hypocreales; Nectriaceae; Fusariumsp. 393 SYM15847 Fungi; Ascomycota; Sordariomycetes; Hypocreales;Nectriaceae; Fusarium udum 394 SYM15870 Fungi; Ascomycota;Sordariomycetes; Hypocreales; Nectriaceae; Fusarium sp. 395 SYM15872Fungi; Ascomycota; Sordariomycetes; Hypocreales; Nectriaceae; Fusariumsp. 396 SYM15890 Fungi; Ascomycota; Dothideomycetes; Capnodiales;Davidiellaceae; Cladosporium sp. 397 SYM15901 Fungi; Ascomycota;Sordariomycetes; Hypocreales; Nectriaceae; Fusarium sp. 398 SYM15920Fungi; Ascomycota; Sordariomycetes; Hypocreales; Nectriaceae; Fusariumequiseti 399 SYM15926 Fungi; Ascomycota; Dothideomycetes; Pleosporales;Pleosporaceae; Alternaria sp. 400 SYM15928 Fungi; Ascomycota;Dothideomycetes; Pleosporales; Pleosporaceae; Alternaria sp. 401SYM15932 Fungi; Ascomycota; Sordariomycetes; Hypocreales; Nectriaceae;Fusarium sp. 402 SYM15939 Fungi; Ascomycota; Sordariomycetes;Hypocreales; Nectriaceae; Fusarium sp. 429 SYM00157 Fungi; Ascomycota;Dothideomycetes; incertae sedis; incertae sedis; Leptosphaerulinachartarum 431 SYM00299 Fungi; Ascomycota; Dothideomycetes; Capnodiales;Davidiellaceae; Cladosporium tenuissimum 432 SYM00301 Fungi; Ascomycota;Eurotiomycetes; Eurotiales; Trichocomaceae; Penicillium chrysogenum 443SYM01324 Fungi; Ascomycota; Eurotiomycetes; Eurotiales; Trichocomaceae;Aspergillus pseudoglaucus 444 SYM01329 Fungi; Ascomycota;Dothideomycetes; Pleosporales; Didymellaceae; Peyronellaea glomerata 445SYM01330 Fungi; Zygomycota; incertae sedis; Mucorales; Rhizopodaceae;Rhizopus oryzae 446 SYM12462 Fungi; Ascomycota; Dothideomycetes;Capnodiales; Davidiellaceae; Cladosporium sphaerospermum 447 SYM15774Fungi; Ascomycota; Dothideomycetes; Pleosporales; Incertae sedis; Phomamedicaginis 448 SYM15783 Fungi; Ascomycota; Dothideomycetes;Pleosporales; Pleosporaceae; Alternaria macrospora 449 SYM00300 Fungi;Ascomycota; Sordariomycetes; Hypocreales; Incertae sedis; Acremoniumstrictum 450 SYM01331 Fungi; Ascomycota; Dothideomycetes; Pleosporales;Incertae sedis; Phoma pedeiae 453 SYM15810 Fungi; Ascomycota;Sordariomycetes; Hypocreales; Nectriaceae; Fusarium sp. 454 SYM15879Fungi; Ascomycota; Sordariomycetes; Hypocreales; Nectriaceae; Fusariumtorulosum 455 SYM15880 Fungi; Ascomycota; Eurotiomycetes; Eurotiales;Trichocomaceae; Penicillium chrysogenum 299 SYM00034 Fungi; Ascomycota;Sordariomycetes; Hypocreales; Incertae sedis; Acremonium zeae

Example 2: Synthetic Compositions Comprising Plant Seeds and a SingleEndophyte Strain or a Plurality of Endophytes Confer Benefits toAgricultural Plants

This example describes the ability of synthetic compositions comprisingplant seeds and a single endophyte strain or a plurality of endophytestrains described herein, to confer one or more benefits to a hostplant. Among other things, this Example describe the ability ofendophytes (e.g., bacterial and fungal endophytes described herein) toconfer beneficial traits on a variety of host plants, including but notlimited to, dicots (e.g., soy, peanut) and monocots (e.g., corn, soy,wheat, cotton, sorghum), and combinations thereof. Endophyte-inoculatedseeds (e.g., seeds described herein) were tested under water-limitedconditions (e.g., drought stress) in seed germination assays andseedling root vigor assays to test whether one or more endophytes conferan increase in tolerance to these stresses. These growth tests wereperformed using growth assays (e.g., germination assays and seedlingroot vigor assays) on sterile filter papers. Seeds were treated eitherwith a single bacterial or fungal strain, or with a combination of twobacterial or two fungal strains. In some embodiments, seeds were treatedwith a combination of at least one bacterial and at least one fungalstrain.

Experimental Description

Growth & Scale-Up of Bacteria for Inoculation

Each bacterial endophyte was streaked out onto 20% Tryptic Soy Agar,forming a lawn on regular Petri dishes (9 cm in diameter). Once thebacteria grew to high density, which happened after one or two daysdepending on the bacterial growth rate, a plate per bacterial strain wasscraped with the aid of a sterile loop (filling the entire hole of theloop and producing a droplet of bacterial biomass of about 20 mg). Thebacteria collected in this way were transferred into 1 ml of sterile 50mM Phosphate Buffer Saline (PBS) in a microcentrifuge tube and fullyresuspended by vortexing for ˜20 sec at maximum speed. This methodachieves highly concentrated (˜0.5-1 optical density, corresponding toabout 108 CFU/mL) and viable bacteria pre-adapted to live coating asurface.

Growth & Scale-Up of Fungi for Inoculation

Fungal isolates were grown from a frozen stock on Petri dishescontaining potato dextrose agar and the plates were incubated at roomtemperature for about a week. After mycelia and spore development, fouragar plugs (1 cm in diameter) were used to inoculate erlenmeyerscontaining 150 ml of potato dextrose broth. Liquid cultures were grownat room temperature and agitation on an orbital shaker at 115 rpm for 4days. Then, the cultures were transferred to 50 ml sterile test tubeswith conical bottoms. Mycelium mats were disrupted by pulse sonicationat 75% setting and 3 pulses of 20 seconds each, using a FisherScientific sonicator (Model FB120) with a manual probe (CL-18). Thesonicated cultures were used in the same manner as the bacterialsuspensions for seed inoculation.

Surface Sterilization of Seeds

Un-treated seeds (e.g., soy seeds or wheat seeds) were sterilizedovernight with chlorine gas as follows: 200 g of seeds were weighed andplaced in a 250 mL glass bottle. The opened bottle and its cap wereplaced in a dessicator jar in a fume hood. A beaker containing 100 mL ofcommercial bleach (8.25% sodium hypochlorite) was placed in thedessicator jar. Immediately prior to sealing the jar, 3 mL ofconcentrated hydrochloric acid (34-37.5%) were carefully added to thebleach. The sterilization was left to proceed for 17-24h. Aftersterilization, the bottle was closed with its sterilized cap, andreopened in a sterile flow hood. The opened bottle was left in thesterile hood for a couple hours to air out the seeds and remove chlorinegas leftover. The bottle was then closed and the seeds stored at roomtemperature in the dark until use.

Preparation of Synthetic Compositions Comprising Plant Seeds andEndophytes

The following procedure was used to coat seeds with a plurality offungal endophyte inocula for planting in greenhouse and field trials.First, 3% Sodium alginate (SA) was prepared and autoclaved in thefollowing manner. Erlenmeyer flasks were filled with the appropriateamount of deionized water and warmed to about 50 degrees C. on a heatplate with agitation using a stirring bar. SA powder was poured slowlyinto the water until it all dissolved. The solution was autoclaved (121°C. @15 PSI for 30 minutes). Talcum powder was autoclaved in dry cycle(121° C. @15 PSI for 30 minutes) and aliquoted in Ziploc bags or 50 mlfalcon tubes at a ratio of 15 g per kg of seed to be treated forformulation controls and 10 g per kg of seed for actual treatments.

The next day, seeds were treated with either powdered or liquidformulations.

For powdered formulations, 10 g per kg of seed was allocated to theseeds to be treated, according to the following procedure. Seeds wereplaced in large plastic container. 16.6 ml of 2% SA per Kg of seeds tobe treated were poured on the seeds. The container was covered andshaken slowly in orbital motion for about 20 seconds to disperse the SA.Endophyte powder was mixed with an equal amount of talcum powder. Themix of endophytes and talc was added on top of the seeds, trying todisperse it evenly. The container was covered and seeds are shakenslowly in orbital motion for about 20 seconds. 13.3 ml of Flo-rite perkg of seed to be treated was poured on the seeds. Seeds were shakenagain, slowly and in orbital motion.

For liquid formulations, 8.5 mL per seed was allocated to the seeds tobe treated, according to the following procedure. Seeds were placed inlarge plastic container. 8.3 ml of 2% SA per kg of seed and the sameamount of bacterial culture (8.3 ml per kg of seed) was poured on theseeds. The container was covered and shaken slowly in orbital motion forabout 20 seconds to disperse the SA. 15 g of talcum powder per kg ofseed was added, trying to disperse it evenly. The container was coveredand seeds were shaken slowly in orbital motion for about 20 seconds.13.3 ml of Flo-rite per kg of seed to be treated are poured on theseeds. Seeds were shaken again, slowly and in orbital motion. For soyseeds, 10 μL of sodium alginate and inoculum were applied for every onegram of seeds. For wheat seeds, the amount of SA and bacterialsuspension or fungal inoculum was adjusted to 15 ml/kg to account forthe larger surface to volume ratio of these small seeds.

Testing for Germination Enhancement Under Drought Stress

Polyethylene glycol (PEG) is an inert, water-binding polymer with anon-ionic and virtually impermeable long chain that accurately mimicsdrought stress under dry-soil conditions. The higher the concentrationof PEG, the lower the water potential achieved, thus inducing higherwater stress in a watery medium. To determine germination enhancement inseeds, the interiors of which are colonized by microbial strains, theeffect of osmotic potential on germination is tested at a range of waterpotential representative of drought conditions following Perez-Fernandezet al. [J. Environ. Biol. 27: 669-685 (2006)]. The range of waterpotentials simulates those that are known to cause drought stress in arange of cultivars and wild plants, (˜0.05 MPa to −5 MPa). Theappropriate concentration of polyethylene glycol (6000) required toachieve a particular water potential was determined following Michel andKaufmann (Plant Physiol., 51: 914-916 (1973)) and further modificationsby Hardegree and Emmerich (Plant Physiol., 92, 462-466 (1990)). Thefinal equation used to determine amounts of PEG is: Ψ=0.130 [PEG]2T−13.7 [PEG] 2; where the osmotic potential (Ψ) is a function oftemperature (T).

Soy Seedling Germination Assay in Drought Conditions

For each SYM tested in the germination assay, ten (10) SYM-coated soyseeds were placed on a 150 mm Petri plate that contained a single heavygermination paper (SD5-¼ 76# heavy weight seed germination paper, AnchorPaper Co., St. Paul, Minn.). To each petri plate, 10 mL 8% polyethyleneglycol (PEG 6000) was added for germination screening assays in droughtconditions. Plates were covered and incubated at in the dark at 22°Celcius and 60% relative humidity for four days for bacterial SYMstrains) or five days for fungal SYM strains. All experiments were donein triplicate under sterile conditions. Seedlings were scored based ongermination percentage relative to formulation only and non-treatedseedling controls at the end of the incubation period. Exemplary soygermination results under drought conditions are shown in Table A.

TABLE A Soy germination assay results Ave (% Crop SYM1 SYM2 toNT) Typesoy SYM00057B 155.83 bacteria soy SYM00074 283.33 bacteria soy SYM00091SYM00092D 120.00 bacterial plurality soy SYM00092D 175.83 bacteria soySYM00590 141.18 bacteria soy SYM00603 135.29 bacteria soy SYM00607SYM00091 115.00 bacterial plurality soy SYM00607 SYM00092D 135.00bacterial plurality soy SYM00619 212.50 bacteria soy SYM00092D SYM15879140.00 Bacterium-Fungus plurality soy SYM00092D SYM15880 115.00Bacterium-Fungus plurality soy SYM00092D SYM15934 115.00Bacterium-Fungus plurarlity soy SYM00299 115.51 fungi soy SYM00301123.02 fungi soy SYM00577 141.18 fungi soy SYM01310 135.29 fungi soySYM01311 135.29 fungi soy SYM01314 135.29 fungi soy SYM01330 325.00fungi soy SYM15774 115.98 fungi soy SYM15783 141.18 fungi soy SYM15879SYM15934 110.00 fungal plurality soy SYM15880 SYM15884 158.82 fungalplurality

Soy Seedling Root Vigor Assay in Drought Conditions

For each SYM tested in the root vigor assay, ten (10) soy seeds wereplaced equidistant to each other on moistened heavy weight germinationpaper sandwiches. Each layer of the germination paper was pre-soaked in25 mL of sterile distilled water. The germination paper sandwich wasrolled, taped using surgical tape, placed in glass bottles and incubatedat 22° Celcius with 60% relative humidity in dark for four (4) days toallow seed germination. On day five (5), bottle lids were removed andseed samples were placed in a growth chamber set to 25° Celcius, 70% RH,250-300 microEinsten light for 12 hours and 18° Celcius, 60% RH dark 12hours for five (5) days. Placement of bottles were randomized daily toreduce any positional effect throughout the incubation period. At theend of the experiment, each soy seedling was measured for total rootlength and compared relative to formulation only and non-treatedseedling controls. Exemplary soy root vigor results under droughtconditions are shown in Table B.

TABLE B Soy root vigor assay results Ave(% SE(% Crop SYM1 SYM2 toNT)toNT) Type soy SYM00057B 98.0 11.9 bacteria soy SYM00074 99.0 10.8bacteria soy SYM00091 SYM00092D 96.7 5.9 bacterial plurality soySYM00092D 87.9 12.9 bacteria soy SYM00590 100.6 11.8 bacteria soySYM00603 118.2 9.3 bacteria soy SYM00607 SYM00091 82.3 5.1 bacterialplurality soy SYM00607 SYM00092D 92.1 8.1 bacterial plurality soySYM00619 99.0 12.4 bacteria soy SYM00092D SYM15879 72.6 8.7 Bacterium -Fungus plurality soy SYM00092D SYM15880 111.2 2.2 Bacterium - Fungusplurality soy SYM00092D SYM15934 82.8 9.7 Bacterium - fungus pluralitysoy SYM00299 92.5 10.0 fungi soy SYM00301 111.3 8.5 fungi soy SYM00577132.4 3.3 fungi soy SYM01310 91.2 15.7 fungi soy SYM01311 97.6 12.3fungi soy SYM01314 107.1 12.3 fungi soy SYM01330 97.6 16.0 fungi soySYM15774 153.7 7.6 fungi soy SYM15783 137.1 7.6 fungi soy SYM15879SYM15934 95.0 12.3 fungal plurality soy SYM15880 SYM15884 104.7 12.3fungal plurality

Wheat Seedling Germination Assay in Drought Conditions

For each SYM tested, 25 uL of sonicated, 7-day old fungal culture or3-day old bacteria culture was added into 15 mL of semi-solid solution[12.5% polyethylene glycol (PEG 6000) and 0.3% of agar] pre-aliquoted ina 90 mm deep well petri dish. After adding the SYM biomass, the petridishes were horizontally shaken for even distribution of SYM biomass.Fifteen (15) surface-steriled wheat seeds were placed onto each petridish. Plates were covered and incubated in the dark at 24° Celcius and60% relative humidity for three days in a Conviron chamber. Allexperiments were done in triplicate under sterile conditions. Seedlingswere scored by counting the number of germinated seedlings per dish andthe performance of each SYM normalized as germination percentagerelative to formulation only and non-treated seedling controls at theend of the incubation period. Exemplary wheat germination results underdrought conditions are shown in Table C.

TABLE C Wheat germination assay results Ave(% SE(% Crop SYM1 SYM2 toNT)toNT) Type wheat SYM00044 126.9 5.5 bacteria wheat SYM00044 SYM00021B150.0 0.0 bacterial plurality wheat SYM00044 SYM00074 136.4 7.9bacterial plurality wheat SYM00044 SYM00879 145.5 18.2 bacterialplurality wheat SYM00044 SYM00879B 136.4 7.9 bacterial plurality wheatSYM00057B 107.4 11.5 bacteria wheat SYM00057B SYM00906 154.5 16.4bacterial plurality wheat SYM00057B SYM01004 136.4 20.8 bacterialplurality wheat SYM00074 109.4 11.0 bacteria wheat SYM00074 SYM00092D131.8 9.1 bacterial plurality wheat SYM00074 SYM00290 131.8 12.0bacterial plurality wheat SYM00074 SYM00879 131.8 12.0 bacterialplurality wheat SYM00074 SYM01004 136.4 7.9 bacterial plurality wheatSYM00074 SYM01022 154.5 16.4 bacterial plurality wheat SYM00092D 118.67.4 bacteria wheat SYM00092D SYM00021B 136.4 13.6 bacterial pluralitywheat SYM00092D SYM00865 135.0 8.7 bacterial plurality wheat SYM00092DSYM00965 150.0 17.3 bacterial plurality wheat SYM00212 157.9 0.0bacteria wheat SYM00290 119.6 6.8 bacteria wheat SYM00290 SYM00906 131.827.6 bacterial plurality wheat SYM00290 SYM01022 145.5 24.1 bacterialplurality wheat SYM00696 108.3 10.1 bacteria wheat SYM00786 SYM00865140.0 18.0 bacterial plurality wheat SYM00879 111.4 7.2 bacteria wheatSYM00879 SYM01004 172.7 4.5 bacterial plurality wheat SYM00879B 105.217.3 bacteria wheat SYM00906 125.0 7.2 bacteria wheat SYM00906 SYM01004136.4 7.9 bacterial plurality wheat SYM00965 SYM00865 150.0 17.3bacterial plurality wheat SYM01004 115.2 12.5 bacteria wheat SYM01004SYM01022 140.9 16.4 bacterial plurality wheat SYM01022 115.5 9.3bacteria wheat SYM01158 142.1 24.1 bacteria wheat SYM01326 103.8 8.5bacteria wheat SYM00157 115.6 10.1 fungi wheat SYM00157 SYM15783 141.711.0 fungal plurality wheat SYM00299 121.4 10.6 fungi wheat SYM00299SYM00696 145.8 11.0 fungal plurality wheat SYM00299 SYM01324 133.3 25.3fungal plurality wheat SYM00299 SYM15783 137.5 0.0 fungal pluralitywheat SYM00301 112.7 10.1 fungi wheat SYM00301 SYM01326 133.3 15.0fungal plurality wheat SYM00301 SYM15774 145.8 11.0 fungal pluralitywheat SYM01324 114.2 8.8 fungi wheat SYM01326 SYM12462 129.2 11.0 fungalplurality wheat SYM12462 SYM15774 133.3 18.2 fungal plurality wheatSYM12462 SYM15783 141.7 16.7 fungal plurality wheat SYM15774 122.4 9.5fungi wheat SYM15774 SYM01324 137.5 12.5 fungal plurality wheat SYM15783120.0 5.4 fungi wheat SYM15783 SYM01324 129.2 8.3 fungal plurality wheatSYM15879 99.4 8.5 fungi wheat SYM15880 SYM15888 159.1 12.0 fungalplurality

Wheat Seedling Root Vigor Assay in Drought Conditions

For each SYM tested, twelve (12) SYM-coated wheat seeds were placed ontoa 125 mm filter paper pre-wet with 5 mL of 12.5% polyethylene glycol(PEG 6000). The seeds were arranged in a circular formation and withembryo facing toward the center of the filter paper. Plates were coveredand incubated in the dark at 24° Celcius and 60% relative humidity forthree days in a Conviron chamber. All experiments were done intriplicate under sterile conditions. At the end of the incubationperiod, images were taken for each plate and root length were measured(in pixel) on the images using ImageJ and the pixel was finallyconverted into cm based on an internal standard. The performance of eachSYM was normalized as root length percentage relative to formulationonly and non-treated seedling controls. Exemplary wheat root vigorresults under drought conditions are shown in Table D.

TABLE D Wheat root vigor assay results Ave(% SE(% Crop SYM1 SYM2 toNT)toNT) Type wheat SYM00021B 104.0 4.4 bacteria wheat SYM00044 101.4 4.0bacteria wheat SYM00044 SYM00021B 111.7 3.7 bacterial plurality wheatSYM00044 SYM00074 101.9 5.1 bacterial plurality wheat SYM00044 SYM00879105.4 4.6 bacterial plurality wheat SYM00044 SYM00879B 107.6 5.0bacterial plurality wheat SYM00057B 102.8 4.6 bacteria wheat SYM00057BSYM00906 118.7 5.4 bacterial plurality wheat SYM00057B SYM01004 104.14.8 bacterial plurality wheat SYM00074 111.2 5.6 bacteria wheat SYM00074SYM00092D 99.5 4.4 bacterial plurality wheat SYM00074 SYM00290 103.5 4.3bacterial plurality wheat SYM00074 SYM00879 107.8 4.6 bacterialplurality wheat SYM00074 SYM01004 110.8 4.7 bacterial plurality wheatSYM00074 SYM01022 102.9 4.7 bacterial plurality wheat SYM00092D 112.13.8 bacteria wheat SYM00092D SYM00021B 103.5 5.8 bacterial pluralitywheat SYM00092D SYM00865 105.2 5.5 bacterial plurality wheat SYM00092DSYM00965 119.2 4.5 bacterial plurality wheat SYM00212 117.7 5.6 bacteriawheat SYM00290 103.2 6.3 bacteria wheat SYM00290 SYM00906 103.1 5.5bacterial plurality wheat SYM00290 SYM01022 112.7 4.0 bacterialplurality wheat SYM00696 162.0 19.6 bacteria wheat SYM00786 SYM00865111.3 4.3 bacterial plurality wheat SYM00879 102.0 4.9 bacteria wheatSYM00879 SYM01004 111.5 5.3 bacterial plurality wheat SYM00879B 102.35.8 bacteria wheat SYM00906 118.3 5.2 bacteria wheat SYM00906 SYM01004111.1 5.3 bacterial plurality wheat SYM00965 SYM00865 111.3 5.5bacterial plurality wheat SYM01004 111.6 4.9 bacteria wheat SYM01004SYM01022 108.2 5.6 bacterial plurality wheat SYM01022 102.1 6.3 bacteriawheat SYM01158 117.0 5.6 bacteria wheat SYM00157 128.1 17.9 fungi wheatSYM00157 SYM15783 234.4 13.5 fungal plurality wheat SYM00299 140.3 11.2fungi wheat SYM00299 SYM00696 47.4 11.5 fungal plurality wheat SYM00299SYM01324 72.6 15.9 fungal plurality wheat SYM00299 SYM15783 90.2 14.2fungal plurality wheat SYM00301 183.7 17.0 fungi wheat SYM00301 SYM0132628.9 8.2 fungal plurality wheat SYM00301 SYM15774 226.9 17.2 fungalplurality wheat SYM01324 181.9 18.5 fungi wheat SYM01326 62.4 14.1 fungiwheat SYM01326 SYM12462 60.4 10.6 fungal plurality wheat SYM01329 195.715.0 fungi wheat SYM01330 102.7 8.2 fungi wheat SYM12462 96.3 15.7 fungiwheat SYM12462 SYM15774 17.6 7.8 fungal plurality wheat SYM12462SYM15783 198.2 16.3 fungal plurality wheat SYM15774 143.4 5.2 fungiwheat SYM15774 SYM01324 102.5 16.2 fungal plurality wheat SYM15783 119.014.8 fungi wheat SYM15783 SYM01324 61.5 13.2 fungal plurality wheatSYM15879 158.9 15.2 fungi wheat SYM15880 SYM15888 148.6 13.3 fungalplurality

Discussion

Plant vigor and improved stress resilience are important components ofproviding fitness to a plant in an agricultural setting. These weremeasured in germination assays and seedling root vigor assays to testthe improvement on plant phenotype as conferred by microbialinoculation. The collection of seed-derived endophytes produced ameasurable response in soy and wheat when inoculated as compared tonon-inoculated controls, as shown in Table A, Table B, Table C and TableD. For example, most of the strains tested were found to produce afavorable phenotype in any of the measured multiple parameters such asgermination efficiency, root length, or shoot length, suggesting thatthe strains play an intimate role modulating and improving plant vigorand conferring stress resilience to the host plant. The stress responsesin the strain collection can be seen by the ability of a subgroup toconfer a beneficial response under different conditions such as waterstress. These can be applicable to products for arid and marginal lands.In a large proportion of cases for the tested strains, the beneficialeffect was measurable in several crops. In one aspect of the invention,it is understood that beneficial strains described herein are capable ofcolonizing multiple varieties and plant species.

Example 3: Synthetic Compositions Comprising Plant Seeds and a SingleEndophyte Strain or a Plurality of Endophyte Strains Confer Benefits toAgricultural Plants

This Example describes the ability of synthetic compositions comprisingplant seeds and a single endophyte strain or a plurality of endophytestrains described herein, to confer beneficial traits to a host plant.Among other things, this Example describe the ability of endophytes(e.g., bacterial and fungal endophytes described herein) to conferbeneficial traits on a variety of host plants, including but not limitedto, dicots (e.g., soy, peanuts) and monocots (e.g., corn, soy, wheat,cotton, sorghum), and combinations thereof. Endophyte-inoculated seeds(e.g., seeds described herein) are tested under normal conditions,biotic stress, heat stress, cold stress, high salt stress, soil withhigh metal content, and combinations thereof, in seed germination assaysand seedling root vigor assays to test whether one or more endophytesconfer an increase in tolerance to one or more stresses. Growth testsare performed using growth assays (e.g., germination assays and seedlingroot vigor assays) on sterile filter papers. In some embodiments, seedsare treated either with a single bacterial or fungal strain, or with acombination of two bacterial or two fungal strains. In some embodiments,seeds are treated with two or more bacterial or fungal strains. In someembodiments, seeds are treated with a combination of at least onebacterial and at least one fungal strain.

Growth and scale-up of bacteria and fungi for inoculation, surfacesterilization of seeds, and seed coating are performed as describedherein.

Testing for Germination Enhancement in Normal Conditions

Standard Germination Tests are used to assess the ability of theendophyte to enhance the seeds' germination and early growth. Briefly,400 seeds (e.g., seeds described herein) are coated with one or moreendophytes described herein, and are placed in between wet brown papertowels (8 replicates with 50 seeds each). An equal number of seeds aretreated with formulation only. Paper towels are placed on top of 1×2feet plastic trays and maintained in a growth chamber set at 25° C. and70% humidity for 7 days. Seedlings are scored based on germinationpercentage relative to formulation only and non-treated seedlingcontrols

Testing for Germination Enhancement Under Biotic Stress

A modification of the method developed by Hodgson [Am. Potato. J. 38:259-264 (1961)] is used to test germination enhancement inmicrobe-colonized seeds under biotic stress. Biotic stress is understoodas a concentration of inocula in the form of cell (bacteria) or sporesuspensions (fungus) of a known pathogen for a particular crop (e.g.,Pantoea stewartii or Fusarium graminearum for Zea mays L.). Briefly, foreach level of biotic stress, 400 seeds (e.g., seeds described herein),the interiors of which are colonized by microbial strains, and 400 seedcontrols (lacking the microbial strains), are placed in between brownpaper towels: 8 replicates with 50 seeds each for each treatment(microbe-colonized and control). Each one of the replicates is placedinside a large petri dish (150 mm in diameter). The towels are thensoaked with 10 mL of pathogen cell or spore suspension at aconcentration of 104 to 108 cells/spores per mL. Each level correspondswith an order of magnitude increment in concentration (thus, 5 levels).The petri dishes are maintained in a growth chamber set at 25° C. and70% humidity for 7 days. The proportion of seeds that germinatesuccessfully is compared between the seeds coming from microbe-colonizedplants with those coming from controls for each level of biotic stress.

Testing for Germination Enhancement in Heat Conditions

Standard Germination Tests are used to determine if a microbe colonizingthe interior of a seed protects maize against heat stress duringgermination. Briefly, 400 seeds (e.g, seeds described herein), theinteriors of which are colonized by microbial strains are placed inbetween wet brown paper towels (8 replicates with 50 seeds each). Anequal number of seeds obtained from control plants that lack the microbeis treated in the same way. The paper towels are placed on top of 1×2 ftplastic trays and maintained in a growth chamber set at 16:8 hourlight:dark cycle, 70% humidity, and at least 120 g/m2/s light intensityfor 7 days. A range of high temperatures (from 35° C. to 45° C., withincrements of 2 degrees per assay) is tested to assess the germinationof microbe-colonized seeds at each temperature. The proportion of seedsthat germinate successfully is compared between the seeds coming frommicrobe-colonized plants and those coming from controls.

Testing for Germination Enhancement in Cold Conditions

Standard Germination Tests are used to determine if a microbe colonizingthe interior of a seed protects maize against cold stress duringgermination. Briefly, 400 seeds (e.g., seeds described herein), theinteriors of which are colonized by microbial strains are placed inbetween wet brown paper towels (8 replicates with 50 seeds each). Anequal number of seeds obtained from control plants that lack the microbeis treated in the same way. The paper towels are placed on top of 1×2 ftplastic trays and maintained in a growth chamber set at 16:8 hourlight:dark cycle, 70% humidity, and at least 120 g/m2/s light intensityfor 7 days. A range of low temperatures (from 0° C. to 10° C., withincrements of 2 degrees per assay) is tested to assess the germinationof microbe-colonized seeds at each temperature. The proportion of seedsthat germinate successfully is compared between the seeds coming frommicrobe-colonized plants and those coming from controls.

Testing for Germination Enhancement in High Salt Concentrations

Germination experiments are conducted in 90 mm diameter petri dishes.Replicates consist of a Petri dish, watered with 10 mL of theappropriate solution and 20 seeds floating in the solution. 400 seeds(e.g., seeds described herein), the interiors of which are colonized bymicrobial strains, and 400 seed controls (lacking the microbial strains)are tested in this way (40 petri dishes total). To prevent largevariations in salt concentration due to evaporation, dishes are sealedwith parafilm and the saline solutions are renewed weekly by pouring outthe existing saline solution in the petri dish and adding the sameamount of fresh solution. A range of saline solutions (100-500 mM NaCl)is tested for to assess the germination of microbe-colonized seeds atvarying salt levels. Petri dishes are maintained in a growth chamber setat 25° C., 16:8 hour light:dark cycle, 70% humidity, and at least 120μE/m2/s light intensity. The proportion of seeds that germinatessuccessfully after two weeks is compared between the seeds coming frominoculated plants and those coming from controls.

Testing for Germination Enhancement in Soils with High Metal Content

Standard Germination Tests are used to determine if a microbe colonizingthe interior of a seed protects maize against stress due to high soilmetal content during germination. Briefly, 400 seeds (e.g., seedsdescribed herein), the interiors of which are colonized by microbialstrains, are placed in between wet brown paper towels (8 replicates with50 seeds each). An equal number of seeds obtained from control plantsthat lack the microbe (microbe-free) is treated in the same way. Thepaper towels are placed on top of 1×2 ft plastic trays with holes toallow water drainage. The paper towels are covered with an inch ofsterile sand. For each metal to be tested, the sand needs to be treatedappropriately to ensure the release and bioavailability of the metal.For example, in the case of aluminum, the sand is watered with pH 4.0+˜1g/Kg soil Al+3 (−621 uM). The trays are maintained in a growth chamberset at 25° C. and 70% humidity for 7 days. The proportion of seeds thatgerminates successfully is compared between the seeds coming frommicrobe-colonized plants and those coming from controls.

Testing for Growth Promotion in Growth Chamber in Normal Conditions

Soil is made from a mixture of 60% Sunshine Mix #5 (Sun Gro; Bellevue,Wash., USA) and 40% vermiculite. To determine if a particular microbecolonizing the interior of seeds is capable of promoting plant growthunder normal conditions, 24 pots are prepared in two 12-pot no-hole flattrays with 28 grams of dry soil in each pot, and 2 L of filtered wateris added to each tray. The water is allowed to soak into the soil andthe soil surface is misted before seeding. For each seed-microbecombination, 12 pots are seeded with 3-5 seeds colonized by the microbeand 12 pots are seeded with 3-5 seeds lacking the microbe (microbe-freeplants). The seeded pots are covered with a humidity dome and kept inthe dark for 3 days, after which the pots are transferred to a growthchamber set at 25° C., 16:8 hour light:dark cycle, 70% humidity, and atleast 120 μE/m2/s light intensity. The humidity domes are removed on day5, or when cotyledons are fully expanded. After removal of the domes,each pot is irrigated to saturation with 0.5× Hoagland's solution, thenallowing the excess solution to drain. Seedlings are then thinned to 1per pot. In the following days, the pots are irrigated to saturationwith filtered water, allowing the excess water to drain after about 30minutes of soaking, and the weight of each 12-pot flat tray is recordedweekly. Canopy area is measured at weekly intervals. Terminal plantheight, average leaf area and average leaf length are measured at theend of the flowering stage. The plants are allowed to dry and seedweight is measured. Significance of difference in growth betweenmicrobe-colonized plants and controls lacking the microbe is assessedwith the appropriate statistical test depending on the distribution ofthe data at p<0.05.

Testing for Growth Promotion in Growth Chamber Under Biotic Stress

Soil is made from a mixture of 60% Sunshine Mix #5 (Sun Gro; Bellevue,Wash., USA) and 40% vermiculite. To determine if a particular microbecolonizing the interior of seeds is capable of promoting plant growth inthe presence of biotic stress, 24 pots are prepared in two 12-potno-hole flat trays with 28 grams of dry soil in each pot, and 2 L offiltered water is added to each tray. The water is allowed to soak intothe soil before planting. For each seed-microbe combination test, 12pots are seeded with 3-5 seeds colonized by the microbe and 12 pots areseeded with 3-5 seeds lacking the microbe (microbe-free plants). Theseeded pots are covered with a humidity dome and kept in the dark for 3days, after which the pots are transferred to a growth chamber set at25° C., 16:8 hour light:dark cycle, 70% humidity, and at least 120μF/m2/s light intensity. The humidity domes are removed on day 5, orwhen cotyledons are fully expanded. After removal of the domes, each potis irrigated to saturation with 0.5× Hoagland's solution, allowing theexcess solution to drain. Seedlings are then thinned to 1 per pot. Inthe following days, the pots are irrigated to saturation with filteredwater, allowing the excess water to drain after about 30 minutes ofsoaking.

Several methods of inoculation are used depending on the lifestyle ofthe pathogen. For leaf pathogens (e.g., Pseudomonas syringeae orColletotrichum graminicola), a suspension of cells for bacteria (108cell/mL) or spores for fungi (107 spores/mL) is applied with anapplicator on the adaxial surface of each of the youngest fully expandedleaves. Alternatively for fungal pathogens that do not form conidiaeasily, two agar plugs containing mycelium (˜4 mm in diameter) areattached to the adaxial surface of each of the youngest leaves on eachside of the central vein. For vascular pathogens (e.g., Pantoeastewartii or Fusarium moniliforme), the suspension of cells or spores isdirectly introduced into the vasculature (5-10 μL) through a minorinjury inflected with a sterile blade. Alternatively, the seedlings canbe grown hydroponically in the cell/spore or mycelium suspension. Totest the resilience of the plant-microbe combination against insectstresses, such as thrips or aphids, plants are transferred to aspecially-designated growth chamber containing the insects. Soil-borneinsect or nematode pathogens are mixed into or applied topically to thepotting soil. In all cases, care is taken to contain the fungal, insect,nematode or other pathogen and prevent release outside of the immediatetesting area.

The weight of each 12-pot flat tray is recorded weekly. Canopy area ismeasured at weekly intervals. Terminal plant height, average leaf areaand average leaf length are measured at the cease of flowering. Theplants are allowed to dry and seed weight is measured. Significance ofdifference in growth between microbe-colonized plants and controlslacking the microbe is assessed with the appropriate statistical testdepending on the distribution of the data at p<0.05.

Example 4—Functional Characterization of Endophytes

Auxin Production Assay

Auxin is an important plant hormone, which can promote cell enlargementand inhibit branch development (meristem activity) in above ground planttissues, while below ground it has the opposite effect, promoting rootbranching and growth. Interestingly, plant auxin is manufactured aboveground and transported to the roots. It thus follows that plant, andespecially root inhabiting microbes which produce significant amounts ofauxin, will be able to promote root branching and development even underconditions where the plant reduces its own production of auxin. Suchconditions can exist for example when soil is flooded and rootsencounter an anoxic environment.

Indole containing IAA is able to generate a pinkish chromophore underacidic conditions in the presence of ferric chloride. For auxinmeasurement, 1 μl of overnight-grown cultures of endophytic bacterialstrains were inoculated into 750 μl of R2A broth supplemented with L-TRP(5 mM) in 2-mL 96 well culture plates. The plates were sealed with abreathable membrane and incubated at 23° C. with constant shaking at 200rpm for 4 days. To measure auxin production by fungal strains, 3 μl of5-day old liquid fungal cultures were inoculated into 1 ml R2A brothsupplemented with L-TRP (5 mM) in 24-well culture plates. The plateswere sealed with breathable tape and incubated at 23° C. with constantshaking at 130 rpm for 4 days. After 4 days, 100 μL of each culture wastransferred to a 96 well plate. 25 μL of Salkowski reagent (1 mL ofFeCl3 0.5 M solution to 50 mL of 35% HClO4) was added into each well andthe plates were incubated in the dark for 30 minutes before takingpicture and measuring 540 nm absorption using the SpectraMax M5 platereader (Molecular Devices). Dark pink halos around colonies arevisualized in the membrane by background illumination using a lighttable.

Endophytes were screened for their ability to produce auxins as possibleroot growth promoting agents. Four replicates were performed for eachstrain assayed. Exemplary auxin production results for endophytesbelonging to core OTUs are presented below in Table E, Table F, andTable G.

Acetoin and Diacetyl Production Assay

For acetoin measurements, microbial strains were cultured as describedabove in R2A broth supplemented with 5% glucose. After 4 days, 100 μL ofeach culture was transferred to a 96 well plate and mixed with 25 μLBarritt's Reagents A and B and 525 nm absorption was measured. Barritt'sReagents A and B were prepared by mixing 5 g/L creatine mixed 3:1 (v/v)with freshly prepared alpha-naphthol (75 g/L in 2.5 M sodium hydroxide).After 15 minutes, plates are scored for red or pink colouration againsta copper coloured negative control. Four replicates were performed foreach strain assayed. Exemplary acetoin production results for endophytesbelonging to core OTUs are presented below in Table E, Table F, andTable G.

Siderophore Production Assay

To ensure no contaminating iron is carried over from previousexperiments, all glassware is deferrated with 6 M HCl and water prior tomedia preparation. For siderophore measurements, microbial strains werecultured as described above in R2A broth. After 3 days of incubation at25° C., plates are overlaid with 0-CAS overlay. Again using the cleanedglassware, 1 liter of 0-CAS overlay is made by mixing 60.5 mg of Chromeazurol S (CAS), 72.9 mg of hexadecyltrimethyl ammonium bromide (HDTMA),30.24 g of finely crushed Piperazine-1,4-bis-2-ethanesulfonic acid(PIPES) with 10 mL of 1 mM FeCl3.6H2O in 10 mM HCl solvent. The PIPEShad to be finely powdered and mixed gently with stirring (not shaking)to avoid producing bubbles, until a dark blue colour is achieved. Melted1% agarose is then added to pre-warmed O-CAS just prior pouring theoverlay in a proportion of 1:3 (v/v). After 15 minutes, colour change isscored by looking for purple halos (catechol type siderophores) ororange colonies (hydroxamate siderophores). Four replicates wereperformed for each strain assayed.

In many environments, iron is a limiting nutrient for growth. A copingmechanism which many microbes have developed is to produce and secreteiron chelating compounds called siderophores which often only thatparticular species or strain has the means to re-uptake and interactwith to release the bound iron, making it available for metabolism. Afringe effect of siderophore production and secretion is that asiderophore secreting microbes can remove all the bio-available iron inits environment, making it difficult for a competing species to invadeand grow in that micro-environment.

Siderophore production by microbes on a plant surface or inside a plantmay both show that a microbe is equipped to grow in a nutrient limitedenvironment, and perhaps protect the plant environment from invasion byother, perhaps undesirable microbes. Exemplary siderophore productionresults for endophytes belonging to core OTUs are presented below inTable E, Table F, and Table G.

TABLE E Auxin, siderophore, and acetoin production by bacterialendophytes belonging to core OTUs; Legend: 0 = no production; 1 = lowproduction; 2 = medium production; 3 = high production Produces SEQSecretes Auxin/ Produces Strain ID NO. siderophores Indoles AcetoinSYM00003 290 2 1 0 SYM00009 291 1 1 0 SYM00013 292 0 1 0 SYM00017A 293 13 0 SYM00018 294 0 3 2 SYM00020 295 0 2 2 SYM00021b 296 0 2 3 SYM00025297 1 3 2 SYM00043 300 1 3 2 SYM00044 301 1 1 3 SYM00050 302 1 2 3SYM00053 303 1 1 2 SYM00062C 305 1 2 1 SYM00068 308 2 2 0 SYM00070 309 22 0 SYM00074 310 2 3 0 SYM00103 311 2 2 2 SYM00183 322 0 2 1 SYM00184323 0 2 0 SYM00207 324 1 2 2 SYM00212 325 2 2 3 SYM00219 326 3 2 3SYM00234 327 2 2 2 SYM00236 328 0 2 0 SYM00248 329 1 2 0 SYM00249 330 22 2 SYM00506c 331 0 2 2 SYM00507 332 1 2 2 SYM00508 333 0 3 2 SYM00525525 2 2 3 SYM00538A 335 3 2 3 SYM00538B 336 2 2 2 SYM00538i 337 0 1 0SYM00543 338 0 3 1 SYM00545 339 2 2 2 SYM00549 340 2 2 2 SYM00563 341 22 1 SYM00574 343 3 1 0 SYM00617 347 1 3 1 SYM00620 348 1 3 0 SYM00627350 0 1 3 SYM00628 351 2 2 3 SYM00646 353 3 2 3 SYM00650 354 2 2 0SYM00662 355 1 1 1 SYM00714 358 1 2 2 SYM00905 365 3 2 2 SYM00924 366 22 2 SYM00963 367 2 2 1 SYM00978 370 2 2 1 SYM00982 368 0 2 3 SYM00987369 1 3 2 SYM00991 371 1 2 2 SYM00999 372 1 1 3 SYM01049 373 1 1 0

TABLE F Auxin, siderophore, and acetoin production by fungal endophytesbelonging to core OTUs; Legend: 0 = no production; 1 = low production; 2= medium production; 3 = high production Produces SEQ Secretes Auxin/Produces Strain ID NO. siderophores Indoles Acetoin SYM00034 299 1 0 0SYM00061A 304 1 0 2 SYM00066 307 1 0 0 SYM00120 312 1 0 0 SYM00122 313 00 0 SYM00123 314 1 0 3 SYM00124 315 1 1 0 SYM00129 316 0 1 0 SYM00135317 0 1 0 SYM00136 318 0 0 1 SYM00151 319 1 1 0 SYM00154 320 0 0 0SYM00566B 342 3 0 0 SYM00577 344 0 0 1 SYM00590 345 0 1 2 SYM00603 346 21 0 SYM00622 349 1 0 2 SYM00629 352 0 1 2 SYM00663 356 2 1 2 SYM00696357 2 0 0 SYM00741b 360 0 0 0 SYM00793 361 1 0 0 SYM00795 362 1 0 1SYM00854 363 2 0 2 SYM00880 364 2 1 2 SYM01300 374 2 1 0 SYM01310 376 02 0 SYM01311 377 0 0 0 SYM01314 378 2 1 0 SYM01315 379 0 0 0 SYM01325380 0 0 2 SYM01326 381 0 0 2 SYM01327 382 2 1 2 SYM01328 383 1 0 0SYM01333 384 0 0 0 SYM15811 385 3 1 0 SYM15820 386 1 0 0 SYM15821 387 10 0 SYM15825 388 0 0 2 SYM15828 389 0 0 2 SYM15831 390 2 1 2 SYM15837391 1 0 0 SYM15839 392 2 0 0 SYM15847 393 0 0 0 SYM15870 394 0 0 0SYM15872 395 0 0 1 SYM15890 396 0 0 2 SYM15901 397 0 0 2 SYM15920 398 20 2 SYM15926 399 1 2 0 SYM15928 400 0 0 0 SYM15932 401 0 0 0 SYM15939402 0 1 0

TABLE G Exemplary siderophore, auxin, and acetoin production ofmicrobial endophytes belonging to core OTUs; SEQ ID Secretes ProducesProduces SYM Taxonomy Type NO. siderophores Auxin/Indoles AcetoinSYM00021B Escherichia sp. bacteria 296 1 1 3 SYM00044 Escherichia sp.bacteria 301 1 1 3 SYM00057b Burkholderia sp. bacteria 426 1 2 3SYM00074 Enterobacter sp. bacteria 310 0 3 0 SYM00091 Agrobacterium sp.bacteria 427 2 2 0 SYM00092D Brevundimonas sp. bacteria 428 3 3 3SYM00157 Leptosphaerulina sp fungi 429 3 1 0 SYM00212 Bacillus sp.bacteria 325 0 0 3 SYM00290 Acinetobacter sp. bacteria 430 1 0 0SYM00300 Acremonium sp. fungi 449 2 0 2 SYM00301 Penicillium sp. fungi432 0 0 2 SYM00577 Acremonium sp. fungi 344 0 0 0 SYM00619Exiguobacterium sp. bacteria 435 0 0 0 SYM00865 Stenotrophomonas sp.bacteria 451 2 1 1 SYM00879 Methylobacterium sp. bacteria 437 0 0 0SYM00879B Sphingomonas sp. bacteria 438 3 1 0 SYM00906 Stenotrophomonassp. bacteria 439 1 1 1 SYM00965 Luteibacter sp. bacteria 440 2 3 3SYM01004 Agrobacterium sp. bacteria 441 1 2 2 SYM01022 Curtobacteriumsp. bacteria 442 3 2 3 SYM01158 Pantoea sp. bacteria 452 1 1 1 SYM01314Fusarium sp. fungi 378 2 1 0 SYM01324 Aspergillus sp. fungi 443 2 1 0SYM01326 Alternaria sp. fungi 381 0 0 0 SYM01329 Phoma sp. fungi 444 1 02 SYM01330 Rhizopus sp. fungi 445 0 0 0 SYM01331 Phoma sp. fungi 450 0 01 SYM12462 Cladosporium sp. fungi 446 0 0 2 SYM15774 Phoma sp. fungi 4470 0 1 SYM15783 Alternaria sp. fungi 448 0 0 2 SYM15810 Fusarium sp.fungi 453 0 2 1 SYM15879 Fusarium sp. fungi 454 0 0 0 SYM15880Penicillium sp. fungi 455 0 0 1 Legend: 0 = no production; 1 = lowproduction; 2 = medium production; 3 = high production

Assay for Growth on Nitrogen Free LGI Media

All glassware is cleaned with 6 M HCl before media preparation. A new 96deep-well plate (2 mL well volume) is filled with 250 ul/well of sterileLGI broth [per L, 50 g Sucrose, 0.01 g FeCl3-6H2O, 0.8 g K3PO4, 0.2 gMgSO₄-7H2O, 0.002 g Na2MoO4-2H2O, pH 7.5]. Microbes are inoculated intothe 96 wells simultaneously with a flame-sterilized 96 pin replicator.The plate is sealed with a breathable membrane, incubated at 28° C.without shaking for 3 days, and OD600 readings taken with a 96 wellplate reader.

A nitrogen fixing plant associated bacterium is able theoretically toadd to the host's nitrogen metabolism, and the most famous beneficialplant associated bacteria, rhizobia, are able to do this withinspecially adapted organs leguminous plant grows for them to be able todo this. In some embodiments, seed associated microbes described hereinare able to fix nitrogen in association with developing seedling,regardless of whether they colonize the plant's surfaces or interior,and thereby add to the plant's nitrogen nutrition.

ACC Deaminase Activity Assay

Microbes are assayed for growth with ACC as their sole source ofnitrogen. Prior to media preparation all glassware is cleaned with 6 MHCl. A 2 M filter sterilized solution of ACC (#1373A, Research Organics,USA) is prepared in water. 1 μl/mL of this is added to autoclaved LGIbroth (see above), and 1 mL aliquots are placed in a new 96 well plate.The plate is sealed with a breathable membrane, incubated at 25° C. withgentle shaking for 5 days, and OD600 readings taken. Only wells that aresignificantly more turbid than their corresponding nitrogen free LGIwells are considered to display ACC deaminase activity.

Plant stress reactions are strongly impacted by the plant's ownproduction and overproduction of the gaseous hormone ethylene. Ethyleneis metabolized from its precursor 1-aminocyclopropane-1-carboxylate(ACC) which can be diverted from ethylene metabolism by microbial andplant enzymes having ACC deaminase activity. As the name implies, ACCdeaminase removes molecular nitrogen from the ethylene precursor,removing it as a substrate for production of the plant stress hormoneand providing for the microbe a source of valuable nitrogen nutrition.

Mineral Phosphate Solubilization Assay

Microbes are plated on tricalcium phosphate media. This is prepared asfollows: 10 g/L glucose, 0.373 g/L NH4NO3, 0.41 g/L MgSO4, 0.295 g/LNaCl, 0.003 FeCl3, 0.7 g/L Ca3HPO4 and 20 g/L Agar, pH 6, thenautoclaved and poured into 150 mm plates. After 3 days of growth at 25°C. in darkness, clear halos are measured around colonies able tosolubilize the tricalcium phosphate.

RNAse Activity Assay

1.5 g of torula yeast RNA (#R6625, Sigma) is dissolved in 1 mL of 0.1 MNa2HPO4 at pH 8, filter sterilized and added to 250 mL of autoclaved R2Aagar media which is poured into 150 mm plates. The bacteria from aglycerol stock plate are inoculated using a flame-sterilized 96 pinreplicator, and incubated at 25° C. for 3 days. On day three, plates areflooded with 70% perchloric acid (#311421, Sigma) for 15 minutes andscored for clear halo production around colonies.

Pectinase Activity Assay

Adapting a previous protocol 0.2% (w/v) of citrus pectin (#76280, Sigma)and 0.1% triton X-100 are added to R2A media, autoclaved and poured into150 mm plates. Bacteria are inoculated using a 96 pin plate replicator.After 3 days of culturing in the darkness at 25° C., pectinase activityis visualized by flooding the plate with Gram's iodine. Positivecolonies are surrounded by clear halos.

Cellulase Activity Assay

Adapting a previous protocol, 0.2% carboxymethylcellulose (CMC) sodiumsalt (#C5678, Sigma) and 0.1% triton X-100 are added to R2A media,autoclaved and poured into 150 mm plates. Bacteria are inoculated usinga 96 pin plate replicator. After 3 days of culturing in the darkness at25° C., cellulose activity is visualized by flooding the plate withGram's iodine. Positive colonies are surrounded by clear halos.

Antibiosis Assay

Bacteria or fungi are inoculated using a 96 pin plate replicator onto150 mm Petri dishes containing R2A agar, then grown for 3 days at 25° C.At this time, colonies of either E. coli DH5a (gram negative tester),Bacillus subtillus ssp. Subtilis (gram positive tester), or yeast strainAH109 (fungal tester) are resuspended in 1 mL of 50 mM Na2HPO4 buffer toan OD600 of 0.2, and 30 μl of this is mixed with 30 mL of warm LB agar.This is quickly poured completely over a microbe array plate, allowed tosolidify and incubated at 37° C. for 16 hours. Antibiosis is scored bylooking for clear halos around microbial colonies.

BIOLOG Characterization of Endophyte Substrate Metabolism

In addition to the auxin, acetoin, and siderophore assays describedabove, endophytes described herein were characterized for their abilityto metabolize a variety of carbon substrates. Liquid cultures of microbewere first sonicated to achieve homogeneity. 1 mL culture of each strainwas harvested by centrifugation for 10 minutes at 4500 RPM andsubsequently washed three times with sterile distilled water to removeany traces of residual media. Microbial samples were resuspended insterile distilled water to a final OD590 of 0.2. Measurements ofabsorbance were taken using a SpectraMax M microplate reader (MolecularDevices, Sunnyvale, Calif.).

Sole carbon substrate assays were done using BIOLOG Phenotype MicroArray(PM) 1 and 2A MicroPlates (Hayward, Calif.). An aliquot of eachbacterial cell culture (2.32 mL) were inoculated into 20 mL sterileIF-0a GN/GP Base inoculating fluid (IF-0), 0.24 mL 100× Dye F obtainedfrom BIOLOG, and brought to a final volume of 24 mL with steriledistilled water. Negative control PM1 and PM2A assays were also madesimilarly minus bacterial cells to detect abiotic reactions. An aliquotof fungal culture (0.05 mL) of each strain were inoculated into 23.95 mLFF-IF medium obtained from BIOLOG. Microbial cell suspensions werestirred in order to achieve uniformity. One hundred microliters of themicrobial cell suspension was added per well using a multichannelpipettor to the 96-well BIOLOG PM1 and PM2A MicroPlates that eachcontained 95 carbon sources and one water-only (negative control) well.

MicroPlates were sealed in paper surgical tape (Dynarex, Orangeburg,N.Y.) to prevent plate edge effects, and incubated stationary at 24° C.in an enclosed container for 70 hours. Absorbance at 590 nm was measuredfor all MicroPlates at the end of the incubation period to determinecarbon substrate utilization for each strain and normalized relative tothe negative control (water only) well of each plate (Garland and Mills,1991; Barua et al., 2010; Siemens et al., 2012; Blumenstein et al.,2015). The bacterial assays were also calibrated against the negativecontrol (no cells) PM1 and PM2A MicroPlates data to correct for anybiases introduced by media on the colorimetric analysis (Borglin et al.,2012). Corrected absorbance values that were negative were considered aszero for subsequent analysis (Garland and Mills, 1991; Blumenstein etal., 2015) and a threshold value of 0.1 and above was used to indicatethe ability of a particular microbial strain to use a given carbonsubstrate (Barua et al., 2010; Blumenstein et al., 2015). Additionally,bacterial MicroPlates were visually examined for the irreversibleformation of violet color in wells indicating the reduction of thetetrazolium redox dye to formazan that result from cell respiration(Garland and Mills, 1991). Fungal PM tests were measured as growthassays and visual observation of mycelial growth in each well was made.Exemplary BIOLOG substrate utilization by endophytes described hereinare presented in Table H, Table I, Table J, Table K, Table L, Table M,Table N, Table O, Table P, Table Q, Table R, Table S, Table T, and TableU.

TABLE H Substrate utilization as determined by BIOLOG PM1 MicroPlates bybacterial endophytes belonging to OTUs present in landrace and wild cornand wheat seeds that are present in lower levels in modern corn andwheat seeds. Strain/Substrate SYM00013 SYM00018 SYM00183 SYM00184SYM00219 SYM00043 D-Serine NO NO NO NO NO NO D-Glucose-6-Phosphate NO NONO NO NO YES L-Asparagine NO NO NO NO NO NO L-glutamine NO NO NO NO NONO Glycyl-L-Aspartic acid YES NO NO NO NO YES Glycyl-L-Glutamic acid NONO YES YES NO NO Glycyl-L-Proline NO NO YES YES NO NO L-Arabinose YESYES NO YES NO YES D-Sorbitol NO NO NO YES NO NO D-Galactonicacid-?-lactone YES YES NO NO YES YES D-Aspartic acid NO NO NO NO NO NOm-Tartaric acid YES YES NO NO NO YES Citric acid NO NO NO NO NO NOTricarballylic acid NO NO NO NO NO NO p-Hydroxy Phenyl acetic acid NO NONO NO NO NO N-Acetyl-D-Glucosamine YES YES YES YES YES YES Glycerol NONO NO NO NO YES D-L-Malic acid NO NO NO YES NO YES D-Glucosaminic acidNO YES NO NO NO YES D-Glucose-1-Phosphate NO YES NO NO NO YES m-InositolNO YES NO YES NO YES L-Serine NO NO NO NO NO NO m-Hydroxy Phenyl Aceticacid NO NO NO NO NO NO D-Saccharic acid NO NO NO YES NO YES L-Fucose NONO NO NO NO NO D-Ribose NO YES YES YES NO YES 1,2-Propanediol NO NO NONO NO NO D-Fructose-6-Phosphate NO YES NO NO NO NO D-Threonine NO NO NONO NO NO L-Threonine NO NO NO NO NO NO Tyramine YES YES YES NO YES NOSuccinic acid NO NO NO NO NO NO D-Glucuronic acid NO NO NO NO NO NOTween 20 NO NO NO YES NO NO Tween 40 NO NO NO NO NO YES Tween 80 NO NOYES YES NO NO Fumaric acid NO NO NO NO NO NO L-Alanine YES YES YES YESYES YES D-Psicose NO YES NO NO NO YES D-Galactose YES YES NO YES YES YESD-Gluconic acid NO YES NO NO NO YES L-Rhamnose NO YES NO NO YES YESa-Keto-Glutaric acid NO NO YES NO NO NO a-Hydroxy Glutaricacid-?-lactone YES NO NO YES NO NO Bromo succinic acid NO NO NO NO NO NOL-Alanyl-Glycine YES YES YES YES NO NO L-Lyxose NO YES NO NO NO YESL-Aspartic acid NO NO YES NO NO NO D-L-a-Glycerol phosphate NO NO NO NONO NO D-Fructose NO NO NO YES NO YES a-Keto-Butyric acid NO NO NO NO NONO a-Hydroxy Butyric acid NO NO NO NO NO NO Propionic acid NO YES NO NONO NO Acetoacetic acid NO NO NO NO NO NO Glucuronamide NO NO NO NO NO NOL-Proline NO YES YES NO NO NO D-Xylose YES YES YES YES NO YES Aceticacid NO YES NO YES NO YES a-Methyl-D-Galactoside NO NO NO NO YES NOβ-Methyl-D-glucoside NO YES NO YES YES YES Mucic acid YES YES YES NO NOYES N-acetyl-β-D-Mannosamine NO NO NO NO NO NO Pyruvic acid NO YES YESYES YES YES D-Alanine YES YES YES YES YES NO L-Lactic acid NO NO NO NONO YES a-D-Glucose NO YES YES YES NO YES a-D-Lactose NO NO YES YES NO NOAdonitol NO YES YES NO NO NO Glycolic acid NO NO NO NO NO NO Mono MethylSuccinate NO NO NO NO NO NO L-Galactonic-acid-?-lactone NO YES YES YESYES YES D-Trehalose NO NO NO NO NO YES Formic acid NO YES NO NO NO YESMaltose NO YES YES YES YES YES Lactulose NO NO YES YES NO NO MaltotrioseNO YES YES YES YES YES Glyoxylic acid NO NO NO NO NO NO Methyl PyruvateNO NO NO NO NO NO D-Galacturonic acid NO NO YES NO NO YES D-Mannose NOYES YES YES NO YES D-Mannitol NO YES NO YES NO YES D-Melibiose NO YESYES YES YES YES Sucrose NO NO YES YES NO YES 2-Deoxy adenosine NO YES NONO NO YES D-Cellobiose NO YES YES YES YES YES D-Malic acid NO NO NO NONO NO Phenylethyl-amine NO NO NO NO NO NO Dulcitol NO NO NO NO YES YESL-Glutamic acid NO NO NO NO NO NO Thymidine NO YES NO NO NO YES UridineYES YES YES YES NO NO Adenosine NO YES NO NO YES YES Inosine NO NO NOYES NO NO L-Malic acid NO NO NO NO NO NO 2-Aminoethanol NO YES YES YESNO NO Strain/Substrate SYM00050 SYM000508 SYM00617 SYM00620 SYM00068SYM00905 D-Serine YES NO NO NO NO NO D-Glucose-6-Phosphate YES YES NOYES NO NO L-Asparagine NO NO NO NO NO NO L-glutamine NO NO NO NO NO NOGlycyl-L-Aspartic acid YES NO NO NO NO NO Glycyl-L-Glutamic acid NO NONO NO YES NO Glycyl-L-Proline YES NO NO NO YES YES L-Arabinose YES NO NONO YES NO D-Sorbitol YES NO NO NO NO NO D-Galactonic acid-?-lactone NONO NO NO NO NO D-Aspartic acid NO NO NO NO NO NO m-Tartaric acid NO NONO NO NO NO Citric acid NO NO NO NO YES NO Tricarballylic acid NO NO NONO NO NO p-Hydroxy Phenyl acetic acid YES NO NO NO NO NON-Acetyl-D-Glucosamine YES NO NO NO NO NO Glycerol YES NO NO NO NO NOD-L-Malic acid NO YES YES NO YES NO D-Glucosaminic acid NO YES NO NO NONO D-Glucose-1-Phosphate YES YES NO NO NO NO m-Inositol YES NO NO NO NONO L-Serine NO NO NO NO NO NO m-Hydroxy Phenyl Acetic acid YES NO NO YESNO NO D-Saccharic acid YES YES NO NO NO NO L-Fucose NO NO NO NO NO NOD-Ribose NO NO NO NO YES NO 1,2-Propanediol NO NO NO NO NO NOD-Fructose-6-Phosphate YES YES NO YES NO NO D-Threonine NO NO NO NO NONO L-Threonine NO NO NO NO NO NO Tyramine NO NO NO NO YES NO Succinicacid NO NO NO NO NO NO D-Glucuronic acid YES NO NO NO NO NO Tween 20 NONO NO NO NO NO Tween 40 NO NO NO NO NO NO Tween 80 NO NO NO NO NO YESFumaric acid NO NO NO NO NO NO L-Alanine YES NO NO YES YES YES D-PsicoseNO NO NO NO NO NO D-Galactose YES YES NO NO NO NO D-Gluconic acid YESYES NO YES NO NO L-Rhamnose YES YES YES YES YES NO a-Keto-Glutaric acidYES NO NO NO YES NO a-Hydroxy Glutaric acid-?-lactone YES NO NO NO YESNO Bromo succinic acid NO NO NO NO NO NO L-Alanyl-Glycine YES NO NO NOYES NO L-Lyxose YES YES NO NO YES NO L-Aspartic acid YES YES NO NO NO NOD-L-a-Glycerol phosphate NO NO NO NO NO NO D-Fructose YES NO NO NO YESNO a-Keto-Butyric acid NO NO NO NO NO NO a-Hydroxy Butyric acid NO NO NONO NO NO Propionic acid NO NO NO NO YES NO Acetoacetic acid NO NO NO NONO NO Glucuronamide NO NO NO NO NO NO L-Proline NO NO NO NO YES NOD-Xylose YES NO NO NO YES NO Acetic acid NO NO NO NO NO NOa-Methyl-D-Galactoside YES NO NO YES NO NO β-Methyl-D-glucoside YES YESNO NO NO NO Mucic acid YES YES NO NO YES NO N-acetyl-β-D-Mannosamine YESNO YES NO NO NO Pyruvic acid YES YES NO NO YES NO D-Alanine NO NO NO NONO NO L-Lactic acid YES NO NO NO NO NO a-D-Glucose YES NO YES NO NO NOa-D-Lactose NO NO NO NO NO NO Adonitol NO NO NO NO NO NO Glycolic acidNO NO NO NO NO NO Mono Methyl Succinate NO NO NO NO NO NOL-Galactonic-acid-?-lactone YES YES NO YES YES NO D-Trehalose YES NO NONO NO NO Formic acid NO NO NO NO NO NO Maltose YES YES YES NO NO YESLactulose NO NO NO NO NO NO Maltotriose YES YES YES NO NO YES Glyoxylicacid NO NO NO NO NO NO Methyl Pyruvate YES YES NO NO YES NOD-Galacturonic acid YES NO NO YES NO NO D-Mannose YES NO NO NO NO YESD-Mannitol YES NO NO NO NO NO D-Melibiose YES NO YES NO NO NO SucroseYES NO NO NO NO NO 2-Deoxy adenosine YES YES NO YES NO NO D-CellobioseYES YES YES NO NO YES D-Malic acid NO NO NO NO YES NO Phenylethyl-amineNO NO NO NO NO NO Dulcitol NO NO YES NO NO NO L-Glutamic acid YES NO NONO NO NO Thymidine YES YES NO NO NO NO Uridine YES YES NO NO NO NOAdenosine NO YES NO YES NO NO Inosine NO NO NO NO NO NO L-Malic acid NONO NO NO NO NO 2-Aminoethanol NO NO NO NO NO NO

TABLE I Substrate utilization as determined by BIOLOG PM2A MicroPlatesby bacterial endophytes belonging to OTUs present in landrace and wildcorn and wheat seeds that are present in lower levels in modern corn andwheat seeds. Strain/Substrate SYM00013 SYM00018 SYM00183 SYM00184SYM00219 SYM00043 N-acetyl-D-Galactosamine NO NO YES YES NO NOGentiobiose NO YES YES YES YES YES D-Raffinose NO NO NO NO YES NO Capricacid NO NO NO NO NO NO D-lactic acid methyl ester NO NO NO NO NO NOAcetamide NO NO NO NO NO NO L-Ornithine YES YES NO YES YES NOChondrointin sulfate C NO NO NO NO NO NO N-acetyl-neuraminic acid NO NONO NO NO NO L-glucose NO NO NO NO NO NO Salicin NO NO YES YES YES NOCaproic acid NO NO NO NO NO NO Malonic acid NO NO NO NO NO NOL-Alaninamide NO NO YES YES NO NO L-Phenylalanine YES NO NO NO NO NOa-Cyclodextrin NO NO NO NO NO NO β-D-allose NO NO NO NO NO NO LactitolNO NO YES YES NO NO Sedoheptulosan NO NO NO NO NO NO Citraconic acid YESNO NO NO NO NO Melibionic acid NO NO NO NO YES NO N-Acetyl-L-Glutamicacid NO NO NO YES NO NO L-Pyroglutamic acid YES YES YES YES YES NOβ-Cyclodextrin NO NO NO NO YES NO Amygdalin NO NO YES YES NO NOD-Melezitose NO NO NO NO NO NO L-Sorbose NO NO NO NO NO NO Citramalicacid NO NO NO NO NO NO Oxalic acid NO NO NO NO NO NO L-Arginine NO NO NONO NO NO L-Valine YES YES NO YES YES NO γ-Cyclodextrin NO NO NO NO YESNO D-arabinose NO NO NO NO NO NO Maltitol NO NO YES YES NO NO StachyoseNO NO NO NO NO NO D-Glucosamine YES YES YES YES YES YES Oxalomalic acidYES YES YES YES NO YES Glycine NO NO NO NO NO NO D,L-Carnitine YES YESNO NO NO NO Dextrin NO NO NO YES YES NO D-arabitol NO NO NO NO NO NOa-Methyl-D-Glucoside NO NO NO NO NO NO D-Tagatose NO NO NO NO NO NO2-Hydroxy benzoic acid NO NO NO NO NO NO Quinic acid NO NO NO NO NO NOL-Histidine NO NO NO NO NO YES Sec-Butylamine NO NO NO NO NO NO GelatinNO NO YES YES NO NO L-arabitol NO NO NO NO NO NO β-Methyl-D-GalactosideNO NO NO YES NO NO Turanose NO NO YES YES NO NO 4-Hydroxy benzoic acidNO NO NO NO NO NO D-Ribono-1,4-Lactone NO NO NO NO NO NO L-Homoserine NONO NO NO NO NO D,L-Octopamine YES YES YES YES YES NO Glycogen NO NO NONO NO NO Arbutin NO NO YES YES YES NO 3-Methyl Glucose NO NO NO NO NO NOXylitol NO NO NO YES NO NO β-Hydroxy butyric acid NO NO NO NO NO NOSebacic acid NO NO NO NO NO NO Hydroxy-L-Proline NO NO NO NO NO NOPutrescine NO YES NO NO NO NO Inulin NO NO YES YES YES YES2-Deoxy-D-Ribose NO NO NO NO NO NO β-Methyl-D-Glucuronic acid NO NO NONO NO NO N-Acetyl-D-glucosaminitol NO NO NO NO NO NO γ-Hydroxy butyricacid NO NO NO NO NO NO Sorbic acid NO NO NO NO NO NO L-Isoleucine YES NONO NO NO NO Dihydroxy acetone NO NO NO YES NO NO Laminarin NO NO NO NONO NO i-Erythritol NO NO NO NO NO NO a-Methyl-D-Manno side NO NO NO NONO NO γ-amino butyric acid YES YES NO NO NO YES a-Keto-valeric acid NONO NO NO NO NO Succinamic acid NO NO NO NO NO NO L-Leucine YES NO NO NONO NO 2,3 -Butanediol YES NO NO NO NO NO Mannan NO NO NO NO NO NO D-Fucose NO NO NO NO NO NO β-Methyl-D-Xyloside NO NO NO NO NO NO d-aminovaleric acid NO NO NO NO NO NO Itaconic acid NO NO NO NO NO NOD-Tartaric acid NO NO NO NO NO NO L-Lysine NO NO NO NO NO NO2,3-Butanone NO NO NO NO NO NO Pectin NO NO NO NO NO NO3-0-β-D-Galactopyranosyl-d- NO NO NO NO NO NO arabinose Palatinose NO NOYES YES YES NO Butyric acid NO NO NO NO NO NO 5-Keto-D-Gluconic acid NOYES NO NO NO YES L-Tartaric acid YES YES NO NO NO YES L-Methionine NO NONO NO NO NO 3-Hydroxy 2-Butanone NO NO NO NO NO NO Strain/SubstrateSYM00050 SYM00508 SYM00617 SYM00620 SYM00068 SYM00905N-acetyl-D-Galactosamine YES NO NO NO NO YES Gentiobiose YES YES YES YESNO YES D-Raffinose YES NO NO YES NO NO Capric acid NO NO NO NO NO NOD-lactic acid methyl ester YES NO NO NO NO NO Acetamide NO NO NO NO YESNO L-Ornithine YES NO NO NO YES NO Chondrointin sulfate C NO NO NO NO NONO N-acetyl-neuraminic acid NO NO NO YES NO NO L-glucose NO NO NO NO NONO Salicin YES YES YES NO NO YES Caproic acid NO YES NO NO NO NO Malonicacid NO NO NO NO NO NO L-Alaninamide NO NO NO NO NO YES L-PhenylalanineNO NO NO NO YES NO a-Cyclodextrin NO NO NO NO NO NO β-D-allose NO NO NONO NO NO Lactitol NO NO NO NO NO YES Sedoheptulosan NO NO NO NO NO NOCitraconic acid NO NO NO NO YES NO Melibionic acid YES NO NO YES YES NON-Acetyl-L-Glutamic acid YES NO NO NO NO NO L-Pyroglutamic acid NO YESNO NO YES NO β-Cyclodextrin NO NO NO NO NO NO Amygdalin NO NO YES NO NONO D-Melezitose NO NO YES NO NO NO L-Sorbose NO NO NO NO NO NOCitramalic acid NO NO NO NO NO NO Oxalic acid NO NO NO NO NO NOL-Arginine NO NO NO NO NO NO L-Valine NO NO NO NO YES NO γ-CyclodextrinNO NO NO NO NO NO D-arabinose NO YES NO NO NO NO Maltitol NO NO NO NO NOYES Stachyose NO NO NO NO NO NO D-Glucosamine YES YES YES NO YES YESOxalomalic acid NO NO YES NO YES YES Glycine NO NO NO NO NO NOD,L-Carnitine NO NO NO NO NO NO Dextrin NO YES YES YES NO NO D-arabitolNO YES NO NO NO NO a-Methyl-D-Glucoside NO NO NO NO NO NO D-Tagatose NOYES NO NO NO NO 2-Hydroxy benzoic acid NO NO NO NO NO NO Quinic acid NONO NO NO NO NO L-Histidine NO NO NO YES NO NO Sec-Butylamine NO NO NO NONO NO Gelatin NO NO NO NO NO YES L-arabitol NO NO NO NO NO NOβ-Methyl-D-Galactoside NO YES NO YES NO NO Turanose NO NO NO NO NO NO4-Hydroxy benzoic acid NO NO NO NO NO NO D-Ribono-1,4-Lactone NO NO NONO NO NO L-Homoserine NO NO NO NO NO NO D,L-Octopamine NO NO YES NO YESYES Glycogen NO YES NO NO NO NO Arbutin YES YES YES NO NO YES 3-MethylGlucose YES NO NO NO NO NO Xylitol NO NO NO NO NO NO β-Hydroxy butyricacid YES YES NO NO NO NO Sebacic acid NO NO NO NO NO NOHydroxy-L-Proline YES NO NO NO NO NO Putrescine YES NO NO NO NO NOInulin NO NO NO NO NO NO 2-Deoxy-D-Ribose NO YES NO YES NO NOβ-Methyl-D-Glucuronic acid NO NO NO NO NO NO N-Acetyl-D-glucosaminitolNO NO NO NO NO NO γ-Hydroxy butyric acid NO NO NO NO NO NO Sorbic acidNO NO NO NO NO NO L-Isoleucine NO YES NO NO YES NO Dihydroxy acetone YESYES NO NO NO NO Laminarin NO NO NO NO NO NO i-Erythritol NO NO NO NO NONO a-Methyl-D-Manno side NO NO NO NO NO NO γ-amino butyric acid NO NO NONO NO NO a-Keto-valeric acid NO NO NO NO NO NO Succinamic acid NO NO NONO NO NO L-Leucine NO NO NO NO NO NO 2,3 -Butanediol NO NO NO NO NO NOMannan NO NO NO NO NO NO D-Fucose NO NO NO NO NO NO β-Methyl-D-XylosideNO NO NO NO NO NO d-amino valeric acid NO NO NO NO NO NO Itaconic acidYES YES NO NO NO NO D-Tartaric acid NO NO NO NO NO NO L-Lysine NO NO NONO NO NO 2,3-Butanone NO NO NO NO NO NO Pectin NO YES NO NO NO NO3-0-β-D-Galactopyranosyl-d- NO NO NO NO NO NO arabinose Palatinose NO NONO NO NO YES Butyric acid NO NO NO NO NO NO 5-Keto-D-Gluconic acid NOYES NO NO NO NO L-Tartaric acid NO YES NO NO NO NO L-Methionine NO NO NONO NO NO 3-Hydroxy 2-Butanone NO NO NO NO NO NO

Twelve SYM strains of culturable bacteria belonging to OTUs present inlandrace and wild corn and wheat seeds that are present in lower levelsin modern corn and wheat seeds were tested for sole carbon substrateutilization using BIOLOG PM1 and PM2A MicroPlates. The most utilizedsubstrates by these strains are L-alanine, L-galactonic-acid-γ-lactone,maltose, maltotriose, D-cellobiose, gentiobiose, and D-glucosamine. Theleast utilized substrates by these strains are L-asparagine,L-glutamine, D-aspartic acid, tricarballylic acid, L-serine, L-fucose,1,2-propanediol, D-threonine, L-threonine, succinic acid, fumaric acid,bromo succinic acid, D-L-a-glycerol phosphate, a-keto-butyric acid,a-hydroxy butyric acid, acetoacetic acid, glucuronamide, glycolic acid,mono methyl succinate, glyoxylic acid, phenylethyl-amine, and L-malicacid.

The substrates most utilized by a large number of the culturablebacteria belonging to core OTUs are mucic acid, L-arabinose,L-galactonic-acid-γ-lactone, N-acetyl-D-glucosamine, maltose,maltotriose, and D-cellobiose. These core bacteria did not utilizesedoheptulosan, oxalic acid, 2-hydroxy benzoic acid, quinic acid,mannan, L-methionine, N-acetyl-D-glucosaminitol, sorbic acid,2,3-butanone, succinic acid, phenylethyl-amine, and 3-hydroxy 2-butanoneas sole carbon sources. Results for the culturable fungi belonging tocore OTUs indicate that D-sorbitol, L-arabinose, N-acetyl-D-glucosamine,glycerol, tween 40, tween 80, D-gluconic acid, L-proline, a-D-glucose,D-trehalose, maltose, lactulose, D-mannose, D-mannitol, sucrose,D-cellobiose, L-glutamic acid, L-ornithine, and L-pyroglutamic acid arecarbon substrates that are utilized by a large number of the endophytestrains examined here. The carbon substrate that seemed to be notutilized by fungi in these assays is 2-deoxy-D-ribose. All othersubstrates could be utilized as a sole carbon nutrient by at least onefungal SYM strain.

TABLE J Substrate utilization as determined by BIOLOG PM1 MicroPlates bybacterial endophytes belonging to core OTUs. Strain/Substrate SYM00103SYM01049 SYM00013 SYM00017A SYM00018 SYM00183 SYM00184 SYM00020 D-SerineNO NO NO NO NO NO NO NO D-Glucose-6-Phosphate NO NO NO YES NO NO NO NOL-Asparagine NO NO NO YES NO NO NO NO L-glutamine NO NO NO NO NO NO NONO Glycyl-L-Aspartic acid NO YES YES NO NO NO NO NO Glycyl-L-Glutamicacid YES NO NO NO NO YES YES NO Glycyl-L-Proline NO NO NO NO NO YES YESNO L-Arabinose NO YES YES YES YES NO YES YES D-Sorbitol NO NO NO YES NONO YES NO D-Galactonic acid-?-lactone NO NO YES YES NO NO NO NOD-Aspartic acid NO NO NO NO NO NO NO NO m-Tartaric acid NO YES YES NOYES NO NO YES Citric acid NO NO NO NO NO NO NO NO Tricarballylic acid NONO NO NO NO NO NO NO p-Hydroxy Phenyl acetic acid NO NO NO YES NO NO NONO N-Acetyl-D-Glucosamine NO NO YES YES YES YES YES YES Glycerol NO NONO YES NO NO NO NO D-L-Malic acid NO NO NO YES NO NO YES NOD-Glucosaminic acid NO NO NO YES YES NO NO YES D-Glucose-1-Phosphate NONO NO YES YES NO NO YES m-Inositol NO NO NO YES YES NO YES YES L-SerineNO NO NO NO NO NO NO NO m-Hydroxy Phenyl Acetic acid NO NO NO NO NO NONO NO D-Saccharic acid NO NO NO YES NO NO YES NO L-Fucose NO NO NO YESNO NO NO NO D-Ribose NO YES NO YES YES YES YES NO 1,2-Propanediol NO NONO NO NO NO NO NO D-Fructose-6-Phosphate NO NO NO YES YES NO NO NOD-Threonine NO NO NO NO NO NO NO NO L-Threonine NO NO NO NO NO NO NO NOTyramine NO NO YES YES YES YES NO YES Succinic acid NO NO NO NO NO NO NONO D-Glucuronic acid NO NO NO NO NO NO NO NO Tween 20 NO NO NO NO NO NOYES NO Tween 40 NO NO NO NO NO NO NO NO Tween 80 YES YES NO NO NO YESYES NO Fumaric acid NO NO NO NO NO NO NO NO L-Alanine YES NO YES YES YESYES YES YES D-Psicose NO NO NO YES YES NO NO YES D-Galactose NO YES YESYES YES NO YES YES D-Gluconic acid YES NO NO NO YES NO NO NO L-RhamnoseNO NO NO YES YES NO NO YES a-Keto-Gutaric acid YES NO NO YES NO YES NONO a-Hydroxy Glutaric acid-?-lactone NO NO YES YES NO NO YES NO Bromosuccinic acid NO NO NO NO NO NO NO NO L-Alanyl-Glycine YES NO YES YESYES YES YES YES L-Lyxose NO NO NO NO YES NO NO YES L-Aspartic acid YESNO NO NO NO YES NO NO D-L-a-Glycerol phosphate NO NO NO NO NO NO NO NOD-Fructose NO NO NO YES NO NO YES YES a-Keto-Butyric acid NO NO NO NO NONO NO NO a-Hydroxy Butyric acid NO NO NO NO NO NO NO NO Propionic acidNO NO NO YES YES NO NO NO Acetoacetic acid NO NO NO NO NO NO NO NOGlucuronamide NO NO NO NO NO NO NO NO L-Proline NO NO NO NO YES YES NONO D-Xylose YES YES YES YES YES YES YES YES Acetic acid NO NO NO YES YESNO YES NO a-Methyl -D-Galactoside NO NO NO YES NO NO NO NOβ-Methyl-D-glucoside NO NO NO YES YES NO YES YES Mucic acid YES YES YESYES YES YES NO YES N-acetyl- β-D-Mannosamine NO NO NO NO NO NO NO NOPyruvic acid NO YES NO YES YES YES YES YES D-Alanine YES NO YES YES YESYES YES YES L-Lactic acid NO NO NO NO NO NO NO NO a-D-Glucose NO YES NOYES YES YES YES NO a-D-Lactose NO NO NO NO NO YES YES NO Adonitol NO NONO YES YES YES NO NO Glycolic acid YES NO NO NO NO NO NO NO Mono MethylSuccinate NO YES NO NO NO NO NO NO L-Galactonic-acid-?-lactone YES YESNO YES YES YES YES YES D-Trehalose YES NO NO YES NO NO NO NO Formic acidNO NO NO NO YES NO NO YES Maltose NO YES NO YES YES YES YES YESLactulose NO NO NO YES NO YES YES NO Maltotriose NO NO NO YES YES YESYES YES Glyoxylic acid NO NO NO NO NO NO NO NO Methyl Pyruvate NO NO NONO NO NO NO NO D-Galacturonic acid YES NO NO YES NO YES NO NO D-MannoseNO YES NO YES YES YES YES NO D-Mannitol NO NO NO YES YES NO YES NOD-Melibiose NO NO NO YES YES YES YES NO Sucrose NO NO NO YES NO YES YESNO 2-Deoxy adenosine NO NO NO NO YES NO NO NO D-Cellobiose NO YES NO YESYES YES YES YES D-Malic acid NO YES NO NO NO NO NO NO Phenylethyl-amineNO NO NO NO NO NO NO NO Dulcitol NO NO NO NO NO NO NO NO L-Glutamic acidNO NO NO NO NO NO NO NO Thymidine NO NO NO NO YES NO NO NO Uridine YESNO YES YES YES YES YES NO Adenosine YES NO NO YES YES NO NO NO InosineNO NO NO NO NO NO YES NO L-Malic acid NO NO NO NO NO NO NO NO2-Aminoethanol YES NO NO YES YES YES YES NO Strain/Substrate SYM00207SYM00212 SYM00219 SYM00234 SYM00236 SYM00248 SYM00249 SYM00260 D-SerineNO NO NO NO NO YES NO NO D-Glucose-6-Phosphate NO YES NO NO NO YES YESNO L-Asparagine NO NO NO NO NO NO YES YES L-glutamine NO NO NO NO NO NOYES NO Glycyl-L-Aspartic acid NO YES NO NO NO NO NO NO Glycyl-L-Glutamicacid YES YES NO NO NO NO NO YES Glycyl-L-Proline NO NO NO NO NO NO NO NOL-Arabinose NO YES NO YES YES YES YES YES D-Sorbitol NO NO NO NO NO NONO NO D-Galactonic acid-?-lactone NO NO YES YES NO YES NO NO D-Asparticacid NO YES NO NO NO NO NO NO m-Tartaric acid NO YES NO NO NO NO NO NOCitric acid NO NO NO NO NO NO YES YES Tricarballylic acid NO YES NO NONO NO NO NO p-Hydroxy Phenyl acetic acid NO NO NO NO NO NO NO NON-Acetyl-D-Glucosamine YES YES YES YES NO YES YES NO Glycerol NO YES NOYES NO YES NO YES D-L-Malic acid YES YES NO YES NO NO NO YESD-Glucosaminic acid NO NO NO NO NO NO NO NO D-Glucose-1-Phosphate NO YESNO NO NO NO YES NO m-Inositol NO YES NO NO NO YES YES YES L-Serine NO NONO NO NO NO NO YES m-Hydroxy Phenyl Acetic acid YES NO NO NO NO NO NO NOD-Saccharic acid NO YES NO NO NO NO NO YES L-Fucose NO YES NO NO NO NONO NO D-Ribose NO YES NO NO NO YES YES NO 1,2-Propanediol NO YES NO NONO NO NO YES D-Fructose-6-Phosphate NO YES NO NO NO NO YES NOD-Threonine NO NO NO NO NO NO NO NO L-Threonine YES NO NO NO NO NO NOYES Tyramine YES YES YES YES NO YES YES NO Succinic acid NO NO NO NO NONO NO NO D-Glucuronic acid NO NO NO NO NO NO YES NO Tween 20 NO NO NO NONO NO NO YES Tween 40 NO NO NO NO NO NO NO YES Tween 80 NO NO NO NO NONO NO YES Fumaric acid NO YES NO NO NO NO NO YES L-Alanine YES YES YESYES YES YES NO YES D-Psicose NO NO NO NO NO NO NO NO D-Galactose NO NOYES NO NO YES YES NO D-Gluconic acid NO YES NO YES NO NO NO YESL-Rhamnose NO YES YES YES NO YES YES NO a-Keto-Gutaric acid YES YES NONO YES NO NO YES a-Hydroxy Glutaric acid-?-lactone NO YES NO NO YES NONO YES Bromo succinic acid NO NO NO NO NO NO NO YES L-Alanyl-Glycine YESYES NO YES NO YES NO YES L-Lyxose NO NO NO NO NO YES NO NO L-Asparticacid YES NO NO NO YES YES YES YES D-L-a-Glycerol phosphate NO NO NO NONO NO NO YES D-Fructose NO YES NO YES NO YES NO NO a-Keto-Butyric acidYES YES NO NO NO NO NO NO a-Hydroxy Butyric acid NO YES NO NO NO NO NOYES Propionic acid YES YES NO NO NO NO NO YES Acetoacetic acid NO NO NONO NO NO NO YES Glucuronamide NO NO NO NO NO NO NO NO L-Proline YES YESNO YES YES YES NO YES D-Xylose NO YES NO YES YES YES NO YES Acetic acidYES YES NO YES YES NO NO YES a-Methyl -D-Galactoside NO YES YES YES NOYES NO NO β-Methyl-D-glucoside NO YES YES YES NO YES YES YES Mucic acidYES YES NO YES NO YES NO YES N-acetyl- β-D-Mannosamine NO NO NO YES NONO NO YES Pyruvic acid YES YES YES YES NO NO YES YES D-Alanine NO NO YESNO NO NO YES NO L-Lactic acid NO NO NO NO NO NO NO YES a-D-Glucose NOYES NO YES NO YES NO NO a-D-Lactose NO YES NO YES NO YES NO NO AdonitolYES NO NO YES NO NO NO NO Glycolic acid YES YES NO NO NO NO NO YES MonoMethyl Succinate YES NO NO YES NO NO NO YES L-Galactonic-acid-?-lactoneYES YES YES YES NO NO NO YES D-Trehalose NO NO NO YES NO YES NO NOFormic acid NO NO NO NO NO YES NO YES Maltose NO YES YES YES NO YES YESYES Lactulose NO YES NO YES NO NO NO NO Maltotriose NO YES YES YES NOYES YES YES Glyoxylic acid NO NO NO NO NO NO NO YES Methyl Pyruvate NOYES NO YES NO NO NO YES D-Galacturonic acid YES NO NO NO NO NO NO YESD-Mannose NO NO NO YES NO YES NO NO D-Mannitol NO NO NO YES NO YES YESYES D-Melibiose NO YES YES YES NO YES NO NO Sucrose NO NO NO YES NO NOYES NO 2-Deoxy adenosine NO NO NO NO NO YES NO YES D-Cellobiose YES YESYES YES NO YES YES YES D-Malic acid NO NO NO NO NO YES NO YESPhenylethyl-amine NO NO NO NO NO NO NO NO Dulcitol NO NO YES NO NO NO NONO L-Glutamic acid NO NO NO NO NO NO NO NO Thymidine YES YES NO YES NONO YES YES Uridine YES YES NO YES NO NO YES YES Adenosine NO YES YES YESNO YES NO YES Inosine YES NO NO YES NO NO NO NO L-Malic acid YES NO NONO NO NO NO YES 2-Aminoethanol NO NO NO YES NO NO NO YES

TABLE K Substrate utilization as determined by BIOLOG PM1 MicroPlates bybacterial endophytes belonging to core OTUs. Strain/Substrate SYM00290SYM00292 SYM00003 SYM00043 SYM00050 SYM05066 SYM00508 SYM00525 SYM00053D-Serine NO YES NO NO YES NO NO NO YES D-Glucose-6- NO NO NO YES YES NOYES NO YES Phosphate L-Asparagine NO NO NO NO NO NO NO NO NO L-glutamineNO NO NO NO NO NO NO NO NO Glycyl-L-Aspartic NO NO NO YES YES NO NO NOYES acid Glycyl-L-Glutamic NO NO NO NO NO NO NO NO NO acidGlycyl-L-Proline NO NO NO NO YES NO NO NO YES L-Arabinose YES YES YESYES YES NO NO NO YES D-Sorbitol NO NO NO NO YES NO NO YES YESD-Galactonic acid-?- NO NO NO YES NO NO NO NO NO lactone D-Aspartic acidNO NO NO NO NO NO NO NO NO m-Tartaric acid NO NO NO YES NO NO NO NO NOCitric acid NO YES NO NO NO NO NO NO NO Tricarballylic acid NO NO NO NONO NO NO NO NO p-Hydroxy Phenyl NO NO NO NO YES NO NO NO NO acetic acidN-Acetyl-D- YES YES YES YES YES NO NO YES YES Glucosamine Glycerol YESYES NO YES YES NO NO NO NO D-L-Malic acid YES YES NO YES NO NO YES YESNO D-Glucosaminic acid NO NO YES YES NO NO YES NO NO D-Glucose-1- NO NONO YES YES NO YES NO NO Phosphate m-Inositol NO YES NO YES YES NO NO YESYES L-Serine NO NO NO NO NO NO NO NO NO m-Hydroxy Phenyl NO NO NO NO YESNO NO NO YES Acetic acid D-Saccharic acid NO YES NO YES YES NO YES NO NOL-Fucose YES NO NO NO NO NO NO NO NO D-Ribose YES YES YES YES NO NO NOYES NO 1,2-Propanediol YES NO NO NO NO NO NO NO NO D-Fructose-6- NO NONO NO YES NO YES NO YES Phosphate D-Threonine YES NO NO NO NO NO NO NONO L-Threonine YES NO NO NO NO NO NO NO NO Tyramine NO YES YES NO NO NONO NO NO Succinic acid NO NO NO NO NO NO NO NO NO D-Glucuronic acid NONO NO NO YES NO NO NO NO Tween 20 YES NO NO NO NO NO NO NO NO Tween 40YES NO NO YES NO NO NO NO NO Tween 80 YES NO NO NO NO NO NO NO NOFumaric acid YES YES NO NO NO NO NO NO NO L-Alanine YES YES YES YES YESNO NO YES YES D-Psicose NO NO NO YES NO NO NO NO NO D-Galactose YES YESNO YES YES NO YES YES NO D-Gluconic acid YES YES NO YES YES NO YES NOYES L-Rhamnose YES YES NO YES YES NO YES YES YES a-Keto-Glutaric acid NOYES NO NO YES NO NO NO YES a-Hydroxy Glutaric NO NO NO NO YES NO NO NONO acid-?-lactone Bromo succinic acid NO YES NO NO NO NO NO NO NOL-Alanyl-Glycine YES YES YES NO YES NO NO YES NO L-Lyxose NO NO NO YESYES NO YES NO NO L-Aspartic acid NO YES NO NO YES NO YES YES NOD-L-a-Glcerol NO NO NO NO NO NO NO NO NO phosphate D-Fructose YES YES NOYES YES NO NO YES YES a-Keto-Butyric acid NO NO NO NO NO NO NO NO NOa-Hydroxy Butyric YES NO NO NO NO NO NO NO NO acid Propionic acid YESYES YES NO NO NO NO NO NO Acetoacetic acid YES YES NO NO NO NO NO NO NOGlucuronamide YES NO NO NO NO NO NO NO NO L-Proline NO YES NO NO NO NONO NO NO D-Xylose YES YES YES YES YES NO NO NO YES Acetic acid YES YESNO YES NO NO NO YES NO a-Methyl-D- YES YES NO NO YES NO NO NO YESGalactoside β-Methyl-D- YES YES NO YES YES NO YES YES YES glucosideMucic acid NO YES YES YES YES NO YES YES YES N-acetyl-β-D- YES YES NO NOYES NO NO NO YES Mannosamine Pyruvic acid YES YES YES YES YES NO YES NONO D-Alanine YES NO NO NO NO NO NO NO NO L-Lactic acid NO YES NO YES YESNO NO NO YES a-D-Glucose YES YES NO YES YES NO NO NO YES a-D-Lactose YESYES NO NO NO NO NO YES NO Adonitol NO NO NO NO NO NO NO NO NO Glycolicacid NO NO NO NO NO NO NO NO NO Mono Methyl YES YES NO NO NO NO NO NO NOSuccinate L-Galactonic- YES YES YES YES YES NO YES YES YESacid-?-lactone D-Trehalose YES YES NO YES YES NO NO NO YES Formic acidNO YES NO YES NO NO NO NO NO Maltose YES YES NO YES YES NO YES YES YESLactulose YES YES NO NO NO NO NO YES NO Maltotriose YES YES NO YES YESNO YES YES YES Glyoxylic acid NO YES YES NO NO NO NO NO NO MethylPyruvate YES YES NO NO YES NO YES NO NO D-Galacturonic acid NO YES NOYES YES NO NO NO NO D-Mannose NO YES NO YES YES NO NO NO YES D-MannitolYES YES NO YES YES NO NO YES YES D-Melibiose YES YES NO YES YES NO NOYES YES Sucrose YES YES NO YES YES NO NO YES YES 2-Deoxy adenosine NOYES NO YES YES NO YES NO YES D-Cellobiose YES YES NO YES YES NO YES YESYES D-Malic acid NO YES NO NO NO NO NO NO NO Phenylethyl-amine NO NO NONO NO NO NO NO NO Dulcitol YES NO NO YES NO NO NO NO NO L-Glutamic acidNO NO NO NO YES NO NO NO NO Thymidine YES YES NO YES YES NO YES NO YESUridine YES YES YES NO YES NO YES YES YES Adenosine YES YES YES YES NONO YES NO NO Inosine NO YES NO NO NO NO NO NO NO L-Malic acid NO YES NONO NO NO NO NO NO 2-Aminoethanol NO NO NO NO NO NO NO NO NOStrain/Substrate SYM00538A SYM00538B SYM005381 SYM00543 SYM00563SYM00574 SYM00057B SYM00617 D-Serine NO NO NO YES NO NO NO NOD-Glucose-6- NO NO NO YES NO NO NO NO Phosphate L-Asparagine NO NO NOYES NO NO NO NO L-glutamine NO NO NO NO NO NO NO NO Glycyl-L-Aspartic NONO NO NO NO NO NO NO acid Glycyl-L-Glutamic NO NO NO YES NO YES NO NOacid Glycyl-L-Proline NO NO NO NO NO NO YES NO L-Arabinose NO YES YESYES YES YES YES NO D-Sorbitol NO NO NO NO NO NO NO NO D-Galactonicacid-?- NO NO NO NO NO NO NO NO lactone D-Aspartic acid NO NO NO NO NONO NO NO m-Tartaric acid NO NO NO NO NO NO NO NO Citric acid NO NO YESYES NO YES NO NO Tricarballylic acid NO NO NO NO NO NO NO NO p-HydroxyPhenyl NO NO NO NO NO NO NO NO acetic acid N-Acetyl-D- YES YES YES YESNO YES NO NO Glucosamine Glycerol NO YES NO YES NO YES NO NO D-L-Malicacid YES YES YES YES NO YES NO YES D-Glucosaminic acid NO NO NO NO NO NONO NO D-Glucose-1- NO NO NO NO NO NO NO NO Phosphate m-Inositol NO YESYES YES NO YES NO NO L-Serine NO NO NO YES NO YES NO NO m-Hydroxy PhenylNO NO NO NO NO NO YES NO Acetic acid D-Saccharic acid NO NO YES YES NOYES NO NO L-Fucose NO NO NO YES NO NO YES NO D-Ribose NO NO NO YES NO NONO NO 1,2-Propanediol NO NO NO NO NO YES NO NO D-Fructose-6- NO NO NO NONO NO NO NO Phosphate D-Threonine NO NO NO NO NO NO NO NO L-Threonine NONO NO YES NO YES NO NO Tyramine NO NO NO YES NO NO NO NO Succinic acidNO NO NO NO NO NO NO NO D-Glucuronic acid NO NO NO NO NO NO NO NO Tween20 NO YES NO NO NO YES YES NO Tween 40 NO NO NO NO NO YES NO NO Tween 80NO NO NO YES NO YES NO NO Fumaric acid NO NO NO NO NO YES NO NOL-Alanine NO NO NO YES NO YES NO NO D-Psicose NO NO NO NO NO NO NO NOD-Galactose NO YES NO NO NO NO YES NO D-Gluconic acid NO YES NO YES NOYES NO NO L-Rhamnose NO YES NO NO YES NO YES YES a-Keto-Glutaric acidYES YES YES YES NO YES NO NO a-Hydroxy Glutaric NO NO YES NO NO YES NONO acid-?-lactone Bromo succinic acid NO NO NO YES NO YES NO NOL-Alanyl-Glycine YES YES YES YES NO YES NO NO L-Lyxose NO NO NO NO NO NONO NO L-Aspartic acid NO YES YES YES NO YES NO NO D-L-a-Glcerol NO NO NONO NO YES NO NO phosphate D-Fructose NO YES NO YES NO NO NO NOa-Keto-Butyric acid NO NO NO NO NO NO NO NO a-Hydroxy Butyric NO NO NONO NO YES NO NO acid Propionic acid NO NO YES NO NO YES NO NOAcetoacetic acid NO NO NO YES NO YES NO NO Glucuronamide NO NO NO NO NONO NO NO L-Proline YES NO YES NO NO YES NO NO D-Xylose NO YES NO NO NOYES NO NO Acetic acid NO YES YES YES NO YES YES NO a-Methyl-D- NO YES NONO NO NO NO NO Galactoside β-Methyl-D- NO YES NO YES NO YES NO NOglucoside Mucic acid NO NO YES YES NO YES YES NO N-acetyl-β-D- NO YES NONO NO YES NO YES Mannosamine Pyruvic acid NO YES NO YES NO YES NO NOD-Alanine NO NO NO NO NO NO YES NO L-Lactic acid NO NO NO YES NO YES NONO a-D-Glucose NO YES NO YES NO NO YES YES a-D-Lactose NO YES NO NO NONO NO NO Adonitol NO NO NO NO NO NO NO NO Glycolic acid NO NO NO NO NOYES NO NO Mono Methyl NO YES NO NO NO YES NO NO Succinate L-Galactonic-YES NO YES NO NO YES NO NO acid-?-lactone D-Trehalose NO YES NO NO NO NONO NO Formic acid NO YES NO YES NO YES YES NO Maltose YES YES NO YES YESYES NO YES Lactulose NO YES NO NO NO NO NO NO Maltotriose YES YES NO YESYES YES NO YES Glyoxylic acid NO NO NO NO NO YES NO NO Methyl PyruvateYES YES NO YES NO YES NO NO D-Galacturonic acid NO YES YES NO NO YES NONO D-Mannose YES YES NO NO YES NO NO NO D-Mannitol NO YES YES NO NO YESNO NO D-Melibiose NO YES NO NO NO NO NO YES Sucrose NO YES YES NO NO NONO NO 2-Deoxy adenosine NO NO NO YES NO YES NO NO D-Cellobiose NO YES NOYES YES YES NO YES D-Malic acid NO NO NO NO NO YES NO NOPhenylethyl-amine NO NO NO NO NO NO NO NO Dulcitol NO NO NO NO NO NO NOYES L-Glutamic acid NO NO NO NO NO NO NO NO Thymidine NO YES NO YES NOYES NO NO Uridine NO YES YES YES NO YES NO NO Adenosine NO YES NO YES NOYES NO NO Inosine YES YES NO YES NO NO NO NO L-Malic acid NO NO NO YESNO YES NO NO 2-Aminoethanol NO YES YES NO NO YES NO NO

TABLE L Substrate utilization as determined by BIOLOG PM1 MicroPlates bybacterial endophytes belonging to core OTUs. Strain/Substrate SYM00620SYM00627 SYM00628 SYM00062C SYM00650 SYM00068 SYM00070 SYM00714 SYM00009D-Serine NO NO YES NO NO NO NO NO NO D-Glucose-6- YES YES YES NO NO NONO YES NO Phosphate L-Asparagine NO NO NO NO NO NO NO NO NO L-glutamineNO NO NO NO NO NO NO NO NO Glycyl-L-Aspartic NO NO NO NO YES NO NO NO NOacid Glycyl-L-Glutamic NO NO NO NO NO YES NO NO NO acid Glycyl-L-ProlineNO NO NO NO NO YES NO NO NO L-Arabinose NO NO YES NO YES YES YES YES YESD-Sorbitol NO NO NO NO NO NO NO YES NO D-Galactonic acid-?- NO YES YESNO NO NO NO YES NO lactone D-Aspartic acid NO NO NO NO NO NO NO NO NOm-Tartaric acid NO NO NO NO NO NO NO NO NO Citric acid NO NO NO NO NOYES NO NO NO Tricarballylic acid NO NO NO NO NO NO NO NO NO p-HydroxyPhenyl NO NO NO NO NO NO NO NO NO acetic acid N-Acetyl-D- NO YES YES NONO NO YES YES NO Glucosamine Glycerol NO NO NO NO NO NO YES YES NOD-L-Malic acid NO NO NO NO NO YES YES YES NO D-Glucosaminic NO NO NO NONO NO NO NO YES acid D-Glucose-1- NO NO NO NO NO NO NO YES NO Phosphatem-Inositol NO NO YES NO NO NO NO YES NO L-Serine NO NO NO NO NO NO NOYES NO m-Hydroxy Phenyl YES NO YES NO NO NO NO NO NO Acetic acidD-Saccharic acid NO NO NO NO NO NO YES YES NO L-Fucose NO NO YES NO NONO YES YES NO D-Ribose NO NO NO NO NO YES YES NO NO 1,2-Propanediol NONO NO NO NO NO NO NO NO D-Fructose-6- YES YES YES NO NO NO YES YES NOPhosphate D-Threonine NO NO NO NO NO NO NO NO NO L-Threonine NO NO NO NONO NO NO NO NO Tyramine NO NO NO NO NO YES YES NO NO Succinic acid NO NONO NO NO NO NO NO NO D-Glucuronic acid NO NO NO NO NO NO NO NO NO Tween20 NO NO NO NO NO NO NO NO NO Tween 40 NO NO NO NO NO NO NO NO NO Tween80 NO NO NO NO NO NO NO NO YES Fumaric acid NO NO NO NO NO NO NO NO NOL-Alanine YES NO YES NO NO YES YES YES NO D-Psicose NO NO NO NO NO NO NOYES NO D-Galactose NO NO YES NO NO NO YES NO NO D-Gluconic acid YES YESNO NO NO NO NO YES NO L-Rhamnose YES YES YES NO YES YES YES YES NOa-Keto-Glutaric acid NO NO NO NO NO YES NO NO NO a-Hydroxy Glutaric NONO NO NO NO YES YES YES NO acid-?-lactone Bromo succinic acid NO NO NONO NO NO NO NO NO L-Alanyl-Glycine NO NO NO NO NO YES YES NO NO L-LyxoseNO NO NO NO NO YES YES YES NO L-Aspartic acid NO NO NO NO NO NO YES YESNO D-L-a-Glycerol NO NO NO NO NO NO NO NO NO phosphate D-Fructose NO NONO NO NO YES YES YES NO a-Keto-Butyric acid NO NO NO NO NO NO NO NO NOa-Hydroxy Butyric NO NO NO NO NO NO NO NO NO acid Propionic acid NO NONO NO NO YES NO YES NO Acetoacetic acid NO NO NO NO NO NO NO NO NOGlucuronamide NO NO NO NO NO NO NO NO NO L-Proline NO NO YES NO NO YESYES NO NO D-Xylose NO YES YES NO YES YES YES YES YES Acetic acid NO NONO NO NO NO YES YES NO a-Methyl-D- YES YES YES NO NO NO NO YES NOGalactoside β-Methyl-D- NO YES YES NO NO NO YES YES NO glucoside Mucicacid NO YES YES NO YES YES YES YES YES N-acetyl-β-D- NO NO YES NO NO NONO NO NO Mannosamine Pyruvic acid NO YES NO NO NO YES NO NO NO D-AlanoneNO NO YES NO NO NO YES NO NO L-Lactic acid NO NO NO NO NO NO NO YES NOa-D-Glucose NO NO NO NO YES NO YES YES NO a-D-Lactose NO NO NO YES NO NONO YES NO Adonitol NO NO NO NO NO NO YES YES NO Glycolic acid NO NO NONO NO NO NO NO NO Mono Methyl NO NO NO NO YES NO NO NO NO SuccinateL-Galactonic- YES YES YES NO NO YES YES YES YES acid-?-lactoneD-Trehalose NO NO NO NO YES NO NO YES NO Formic acid NO YES NO NO NO NOYES YES NO Maltose NO YES YES YES YES NO YES YES NO Lactulose NO NO NOYES NO NO NO YES NO Maltotriose NO YES YES NO NO NO YES YES NO Glyoxylicacid NO NO NO NO NO NO NO NO NO Methyl Pyruvate NO NO NO NO NO YES NO NONO D-Galacturonic acid YES NO NO NO NO NO NO YES NO D-Mannose NO NO NONO NO NO NO YES NO D-Mannitol NO NO NO NO NO NO NO YES NO D-Melibiose NOYES YES YES NO NO YES YES NO Sucrose NO YES NO NO NO NO NO NO NO 2-Deoxyadenosine YES YES YES NO NO NO YES NO NO D-Cellobiose NO YES YES NO NONO NO YES NO D-Malic acid NO NO NO NO YES YES NO YES NOPhenylethyl-amine NO NO NO NO NO NO NO NO NO Dulcitol NO YES NO YES NONO NO NO NO L-Glutamic acid NO NO NO NO NO NO NO NO NO Thymidine NO YESYES YES NO NO NO NO NO Uridine NO NO YES NO NO NO YES NO YES AdenosineYES NO YES NO NO NO NO NO NO Inosine NO NO NO NO NO NO NO YES NO L-Malicacid NO NO NO NO NO NO NO YES NO 2-Aminoethanol NO NO NO NO NO NO NO NONO Strain/Substrate SYM00905 SYM00924 SYM00963 SYM00978 SYM00982SYM00987 SYM00991 SYM00999 D-Serine NO NO NO YES NO NO YES NOD-Glucose-6- NO NO NO NO NO NO YES NO Phosphate L-Asparagine NO NO NO NONO NO NO NO L-glutamine NO NO NO NO NO NO NO NO Glycyl-L-Aspartic NO NONO NO NO NO NO NO acid Glycyl-L-Glutamic NO NO NO NO NO NO NO NO acidGlycyl-L-Proline YES NO NO NO NO NO NO NO L-Arabinose NO NO NO NO NO YESNO YES D-Sorbitol NO NO NO NO NO NO NO NO D-Galactonic acid-?- NO NO NONO NO NO NO NO lactone D-Aspartic acid NO NO NO NO NO NO NO NOm-Tartaric acid NO NO NO NO NO NO NO NO Citric acid NO NO NO NO NO NO NONO Tricarballylic acid NO NO NO NO NO NO NO NO p-Hydroxy Phenyl NO NO NONO NO YES NO NO acetic acid N-Acetyl-D- NO NO NO NO NO YES NO NOGlucosamine Glycerol NO NO NO NO NO NO NO NO D-L-Malic acid NO NO NO NOYES NO NO NO D-Glucosaminic NO NO NO NO NO NO NO NO acid D-Glucose-1- NONO NO NO NO NO NO NO Phosphate m-Inositol NO NO NO NO NO NO NO NOL-Serine NO NO NO NO NO NO NO NO m-Hydroxy Phenyl NO NO NO NO NO NO NONO Acetic acid D-Saccharic acid NO NO NO NO NO YES NO YES L-Fucose NO NOYES YES NO NO NO NO D-Ribose NO NO NO NO NO NO NO NO 1,2-Propanediol NONO NO NO NO NO NO NO D-Fructose-6- NO YES NO NO NO NO YES NO PhosphateD-Threonine NO NO NO NO NO NO NO NO L-Threonine NO NO NO NO NO NO NO NOTyramine NO NO NO NO NO NO NO NO Succinic acid NO NO NO NO NO NO NO NOD-Glucuronic acid NO NO NO NO NO NO NO NO Tween 20 NO NO NO NO NO NO NONO Tween 40 NO NO NO NO NO NO NO NO Tween 80 YES NO YES NO NO YES NO NOFumaric acid NO NO NO NO NO NO NO NO L-Alanine YES NO NO NO NO NO NO NOD-Psicose NO NO NO NO NO NO NO NO D-Galactose NO NO NO NO NO NO NO NOD-Gluconic acid NO NO NO NO NO NO NO NO L-Rhamnose NO NO NO NO NO NO NONO a-Keto-Glutaric acid NO NO NO NO NO YES YES YES a-Hydroxy Glutaric NONO NO NO NO NO NO NO acid-?-lactone Bromo succinic acid NO NO NO NO NONO NO NO L-Alanyl-Glycine NO NO NO NO NO NO NO NO L-Lyxose NO NO NO NONO NO NO NO L-Aspartic acid NO YES NO NO NO NO NO NO D-L-a-Glycerol NONO NO NO NO NO NO NO phosphate D-Fructose NO NO NO NO NO NO NO NOa-Keto-Butyric acid NO NO NO NO NO NO NO NO a-Hydroxy Butyric NO NO NONO NO NO NO NO acid Propionic acid NO NO YES NO NO NO NO NO Acetoaceticacid NO NO NO NO NO NO NO NO Glucuronamide NO NO NO NO NO NO NO NOL-Proline NO NO NO NO NO NO NO NO D-Xylose NO NO NO NO NO NO NO NOAcetic acid NO NO NO NO YES NO NO NO a-Methyl-D- NO NO YES NO NO NO NONO Galactoside β-Methyl-D- NO NO NO NO NO NO NO NO glucoside Mucic acidNO NO YES NO NO YES NO YES N-acetyl-β-D- NO NO NO YES NO NO YES NOMannosamine Pyruvic acid NO NO NO NO NO NO NO NO D-Alanone NO NO NO NONO NO NO NO L-Lactic acid NO NO NO NO NO YES NO NO a-D-Glucose NO NO NONO NO YES YES NO a-D-Lactose NO NO YES NO NO NO NO NO Adonitol NO NO NONO NO NO NO NO Glycolic acid NO NO NO NO NO NO NO NO Mono Methyl NO YESNO NO NO NO NO YES Succinate L-Galactonic- NO NO NO NO NO YES NO NOacid-?-lactone D-Trehalose NO NO NO NO NO NO NO NO Formic acid NO NO NONO NO NO NO NO Maltose YES NO YES NO NO NO YES NO Lactulose NO NO YES NONO YES NO NO Maltotriose YES NO YES NO NO NO NO NO Glyoxylic acid NO YESNO NO NO NO NO YES Methyl Pyruvate NO NO YES NO NO NO NO YESD-Galacturonic acid NO NO NO NO NO NO NO NO D-Mannose YES NO NO NO NO NONO NO D-Mannitol NO NO NO NO NO NO NO NO D-Melibiose NO NO NO NO NO NONO NO Sucrose NO NO NO NO NO YES YES NO 2-Deoxy adenosine NO NO NO NO NONO NO NO D-Cellobiose YES NO NO NO NO NO NO NO D-Malic acid NO NO YES NONO NO NO NO Phenylethyl-amine NO NO NO NO NO NO NO NO Dulcitol NO NO YESNO NO NO NO NO L-Glutamic acid NO NO NO NO NO NO NO NO Thymidine NO NOYES NO NO NO NO NO Uridine NO NO NO NO NO NO NO NO Adenosine NO NO NO NONO NO NO NO Inosine NO NO NO NO NO NO NO NO L-Malic acid NO NO NO NO NONO NO NO 2-Aminoethanol NO NO NO NO NO NO NO NO

TABLE M Substrate utilization as determined by BIOLOG PM2A MicroPlatesby bacterial endophytes belonging to core OTUs. Strain/SubstrateSYM00103 SYM01049 SYM00013 SYM00017A SYM00018 SYM00183 SYM00184 SYM00020N-acetyl-D-Galactosamine NO NO NO YES NO YES YES NO Gentiobiose NO NO NOYES YES YES YES YES D-Raffinose NO NO NO YES NO NO NO NO Capric acid NONO NO NO NO NO NO NO D-lactic acid methyl ester NO NO NO NO NO NO NO NOAcetamide NO NO NO NO NO NO NO NO L-Ornithine YES NO YES YES YES NO YESYES Chondrointin sulfate C NO NO NO NO NO NO NO NO N-acetyl-neuraminicacid NO NO NO NO NO NO NO NO L-glucose NO NO NO NO NO NO NO NO SalicinNO NO NO YES NO YES YES NO Caproic acid NO NO NO NO NO NO NO NO Malonicacid NO NO NO NO NO NO NO NO L-Alaninamide NO NO NO NO NO YES YES NOL-Phenylalanine NO NO YES NO NO NO NO NO a-Cyclodextrin NO NO NO NO NONO NO NO β-D-allose NO NO NO YES NO NO NO NO Lactitol NO NO NO YES NOYES YES NO Sedoheptulosan NO NO NO NO NO NO NO NO Citraconic acid NO NOYES NO NO NO NO NO Melibionic acid NO NO NO YES NO NO NO NON-Acetyl-L-Glutamic acid YES NO NO YES NO NO YES NO L-Pyroglutamic acidYES NO YES YES YES YES YES YES β-Cyclodextrin NO NO NO NO NO NO NO NOAmygdalin NO NO NO NO NO YES YES NO D-Melezitose NO NO NO NO NO NO NO NOL-Sorbose NO NO NO NO NO NO NO NO Citramalic acid NO NO NO NO NO NO NONO Oxalic acid NO NO NO NO NO NO NO NO L-Arginine NO NO NO YES NO NO NONO L-Valine YES NO YES YES YES NO YES YES γ-Cyclodextrin NO NO NO NO NONO NO NO D-arabinose NO NO NO NO NO NO NO NO Maltitol NO NO NO YES NOYES YES NO Stachyose NO NO NO NO NO NO NO NO D-Glucosamine YES YES YESYES YES YES YES YES Oxalomalic acid YES NO YES YES YES YES YES YESGlycine NO NO NO NO NO NO NO NO D,L-Carnitine YES YES YES YES YES NO NONO Dextrin NO NO NO NO NO NO YES NO D-arabitol NO NO NO NO NO NO NO NOa-Methyl-D-Glucoside NO NO NO NO NO NO NO NO D-Tagatose NO NO NO NO NONO NO NO 2-Hydroxy benzoic acid NO NO NO NO NO NO NO NO Quinic acid NONO NO NO NO NO NO NO L-Histidine NO YES NO NO NO NO NO NO Sec-ButylamineNO NO NO NO NO NO NO NO Gelatin NO NO NO NO NO YES YES NO L-arabitol NONO NO NO NO NO NO NO β-Methyl-D-Galactoside NO NO NO YES NO NO YES NOTuranose NO YES NO YES NO YES YES NO 4-Hydroxy benzoic acid NO NO NO NONO NO NO NO D-Ribono-1,4-Lactone NO NO NO YES NO NO NO NO L-HomoserineNO NO NO NO NO NO NO NO D,L-Octopamine YES NO YES YES YES YES YES YESGlycogen NO NO NO NO NO NO NO NO Arbutin NO NO NO YES NO YES YES NO3-Methyl Glucose NO NO NO NO NO NO NO NO Xylitol NO NO NO NO NO NO YESNO β-Hydroxy butyric acid NO NO NO NO NO NO NO NO Sebacic acid YES NO NONO NO NO NO NO Hydroxy-L-Proline NO NO NO NO NO NO NO NO Putrescine YESNO NO YES YES NO NO NO Inulin NO NO NO YES NO YES YES NO2-Deoxy-D-Ribose NO NO NO NO NO NO NO NO β-Methyl-D-Glucuronic acid NONO NO NO NO NO NO NO N-Acetyl-D-glucosaminitol NO NO NO NO NO NO NO NOγ-Hydroxy butyric acid NO NO NO NO NO NO NO NO Sorbic acid NO NO NO NONO NO NO NO L-Isoleucine YES NO YES YES NO NO NO NO Dihydroxy acetone NOYES NO NO NO NO YES NO Laminarin NO NO NO NO NO NO NO NO i-Erythritol NONO NO NO NO NO NO NO a-Methyl-D-Mannoside NO NO NO NO NO NO NO NOγ-amino butyric acid YES YES YES YES YES NO NO NO a-Keto-valeric acid NONO NO NO NO NO NO NO Succinamic acid NO YES NO NO NO NO NO NO L-LeucineYES NO YES YES NO NO NO NO 2,3-Butanediol NO NO YES NO NO NO NO NOMannan NO NO NO NO NO NO NO NO D-Fucose NO NO NO NO NO NO NO NOB-Methyl-D-Xyloside NO NO NO YES NO NO NO NO d-amino valeric acid NO NONO NO NO NO NO NO Itaconic acid NO NO NO NO NO NO NO NO D-Tartaric acidNO NO NO NO NO NO NO NO L-Lysine NO NO NO NO NO NO NO NO 2,3-Butanone NONO NO NO NO NO NO NO Pectin NO NO NO NO NO NO NO NO3-0-β-D-Galactopyranosyl- NO NO NO NO NO NO NO NO D-arabinose PalatinoseNO NO NO YES NO YES YES NO Butyric acid NO NO NO NO NO NO NO NO5-Keto-D-Gluconic acid NO NO NO NO YES NO NO YES L-Tartaric acid YES NOYES NO YES NO NO YES L-Methionine NO NO NO NO NO NO NO NO 3-Hydroxy2-Butanone NO NO NO NO NO NO NO NO Strain/Substrate SYM00207 SYM00212SYM00219 SYM00234 SYM00236 SYM00248 SYM00249 N-acetyl-D-Galactosamine NONO NO NO NO NO NO Gentiobiose NO YES YES YES NO YES YES D-Raffinose NOYES YES YES NO YES YES Capric acid YES NO NO NO NO NO NO D-lactic acidmethyl ester NO NO NO NO NO NO NO Acetamide NO NO NO NO NO NO NOL-Ornithine YES YES YES YES YES NO NO Chondrointin sulfate C NO NO NO NONO NO NO N-acetyl-neuraminic acid NO NO NO NO NO NO NO L-glucose NO NONO NO NO YES NO Salicin NO YES YES YES NO NO YES Caproic acid YES NO NONO NO NO NO Malonic acid NO NO NO NO NO NO NO L-Alaninamide NO NO NO NOYES NO YES L-Phenylalanine NO NO NO NO NO NO NO a-Cyclodextrin NO YES NOYES NO NO NO β-D-allose NO NO NO NO NO NO NO Lactitol NO NO NO YES NOYES NO Sedoheptulosan NO NO NO NO NO NO NO Citraconic acid NO NO NO NONO NO NO Melibionic acid NO YES YES NO NO YES NO N-Acetyl-L-Glutamicacid NO NO NO YES NO NO NO L-Pyroglutamic acid YES YES YES YES YES YESNO β-Cyclodextrin NO NO YES YES NO NO YES Amygdalin NO YES NO YES NO YESYES D-Melezitose NO YES NO YES NO YES YES L-Sorbose NO NO NO NO NO NO NOCitramalic acid NO NO NO NO NO NO NO Oxalic acid NO NO NO NO NO NO NOL-Arginine NO NO NO NO NO NO NO L-Valine NO YES YES YES NO NO NOγ-Cyclodextrin NO NO YES YES NO NO NO D-arabinose NO NO NO NO NO NO NOMaltitol NO YES NO YES NO YES YES Stachyose NO YES NO YES NO NO NOD-Glucosamine NO YES YES YES YES YES YES Oxalomalic acid NO NO NO YESYES YES YES Glycine NO NO NO NO NO NO YES D,L-Carnitine NO NO NO YES NONO YES Dextrin NO NO YES YES NO NO NO D-arabitol YES NO NO NO NO NO NOa-Methyl-D-Glucoside NO NO NO YES YES NO YES D-Tagatose NO NO NO NO NONO YES 2-Hydroxy benzoic acid NO NO NO NO NO NO NO Quinic acid NO NO NONO NO NO NO L-Histidine YES YES NO NO NO NO NO Sec-Butylamine NO NO NONO NO NO YES Gelatin YES NO NO YES NO NO YES L-arabitol NO NO NO NO NONO NO β-Methyl-D-Galactoside NO NO NO YES NO NO NO Turanose NO YES NOYES NO NO YES 4-Hydroxy benzoic acid NO NO NO NO NO NO NOD-Ribono-1,4-Lactone NO NO NO NO NO NO NO L-Homoserine YES NO NO NO NONO NO D,L-Octopamine NO NO YES YES YES NO NO Glycogen NO NO NO YES NO NONO Arbutin NO YES YES YES NO YES YES 3-Methyl Glucose NO NO NO NO NO NONO Xylitol NO NO NO YES NO NO NO β-Hydroxy butyric acid NO NO NO NO NONO NO Sebacic acid NO NO NO NO YES NO NO Hydroxy-L-Proline NO NO NO NOYES NO YES Putrescine NO YES NO NO NO NO NO Inulin NO NO YES NO NO YESYES 2-Deoxy-D-Ribose NO NO NO NO NO NO NO β-Methyl-D-Glucuronic acid NONO NO NO NO NO NO N-Acetyl-D-glucosaminitol NO NO NO NO NO NO NOγ-Hydroxy butyric acid NO NO NO NO NO NO NO Sorbic acid NO NO NO NO NONO NO L-Isoleucine YES YES NO YES NO NO NO Dihydroxy acetone NO NO NO NONO NO NO Laminarin NO NO NO YES NO NO NO i-Erythritol YES NO NO NO NO NONO a-Methyl-D-Mannoside NO NO NO NO NO NO NO γ-amino butyric acid NO NONO YES NO NO YES a-Keto-valeric acid NO NO NO NO NO NO NO Succinamicacid NO YES NO NO NO NO NO L-Leucine YES NO NO YES NO NO NO2,3-Butanediol NO NO NO YES NO NO NO Mannan NO NO NO NO NO NO NOD-Fucose NO NO NO NO NO NO NO B-Methyl-D-Xyloside NO NO NO YES NO NO NOd-amino valeric acid NO NO NO NO YES NO NO Itaconic acid YES YES NO NONO NO NO D-Tartaric acid NO NO NO NO NO NO NO L-Lysine NO NO NO NO NO NONO 2,3-Butanone NO NO NO NO NO NO NO Pectin NO NO NO YES NO NO NO3-0-β-D-Galactopyranosyl- NO NO NO YES NO NO NO D-arabinose PalatinoseNO YES YES YES NO NO NO Butyric acid YES NO NO NO NO NO NO5-Keto-D-Gluconic acid NO NO NO NO NO NO NO L-Tartaric acid NO NO NO NONO NO NO L-Methionine NO NO NO NO NO NO NO 3-Hydroxy 2-Butanone NO NO NONO NO NO NO

TABLE N Substrate utilization as determined by BIOLOG PM2A MicroPlatesby bacterial endophytes belonging to core OTUs. Strain/SubstrateSYM00260 SYM00290 SYM00292 SYM00003 SYM00043 SYM00050 SYM05066 SYM00508SYM00525 N-acetyl-D- NO NO NO NO NO YES NO NO NO GalactosamineGentiobiose YES YES YES NO YES YES NO YES YES D-Raffinose YES YES YES NONO YES NO NO NO Capric acid NO NO NO NO NO NO NO NO NO D-lactic acid NONO NO NO NO YES NO NO NO methyl ester Acetamide NO NO NO NO NO NO NO NONO L-Ornithine YES NO NO YES NO YES NO NO NO Chondrointin YES NO NO NONO NO NO NO NO sulfate C N-acetyl- NO NO NO NO NO NO NO NO NO neuraminicacid L-glucose NO NO NO NO NO NO NO NO NO Salicin YES YES YES NO NO YESNO YES YES Caproic acid YES NO YES NO NO NO NO YES NO Malonic acid YESNO NO NO NO NO NO NO YES L-Alaninamide NO YES NO NO NO NO NO NO YESL-Phenylalanine YES NO NO YES NO NO NO NO NO a-Cyclodextrin NO YES YESNO NO NO NO NO NO β-D-allose NO NO YES NO NO NO NO NO NO Lactitol NO YESYES NO NO NO NO NO YES Sedoheptulosan NO NO NO NO NO NO NO NO NOCitraconic acid NO NO NO YES NO NO NO NO NO Melibionic acid YES NO NO NONO YES NO NO NO N-Acetyl-L- YES NO YES NO NO YES NO NO NO Glutamic acidL-Pyroglutamic YES NO YES YES NO NO NO YES YES acid β-Cyclodextrin NOYES YES NO NO NO NO NO NO Amygdalin NO YES YES NO NO NO NO NO YESD-Melezitose NO YES YES NO NO NO NO NO YES L-Sorbose NO NO NO NO NO NONO NO NO Citramalic acid YES NO YES NO NO NO NO NO NO Oxalic acid NO NONO NO NO NO NO NO NO L-Arginine YES NO NO NO NO NO NO NO NO L-Valine YESNO YES YES NO NO NO NO NO γ-Cyclodextrin NO YES YES NO NO NO NO NO NOD-arabinose NO YES YES NO NO NO NO YES NO Maltitol NO YES YES NO NO NONO NO YES Stachyose YES YES YES NO NO NO NO NO YES D-Glucosamine YES YESYES YES YES YES NO YES YES Oxalomalic acid YES YES YES YES YES NO YES NOYES Glycine NO NO NO NO NO NO NO NO NO D,L-Carnitine NO NO NO YES NO NONO NO NO Dextrin YES YES YES NO NO NO NO YES YES D-arabitol NO NO YES NONO NO NO YES NO a-Methyl-D- NO YES YES NO NO NO NO NO NO GlucosideD-Tagatose NO YES NO NO NO NO NO YES NO 2-Hydroxy NO NO NO NO NO NO NONO NO benzoic acid Quinic acid NO NO NO NO NO NO NO NO NO L-HistidineYES YES NO NO YES NO NO NO NO Sec-Butylamine NO NO NO NO NO NO NO NO NOGelatin YES YES YES NO NO NO NO NO NO L-arabitol NO NO NO NO NO NO NO NONO β-Methyl-D- NO YES YES NO NO NO NO YES YES Galactoside Turanose NOYES YES NO NO NO NO NO YES 4-Hydroxy NO NO NO NO NO NO NO NO NO benzoicacid D-Ribono-1,4- NO NO NO NO NO NO NO NO NO Lactone L-Homoserine NO NONO NO NO NO NO NO NO D,L-Octopamine NO NO NO YES NO NO YES NO NOGlycogen YES YES YES NO NO NO NO YES NO Arbutin NO YES YES NO NO YES NOYES YES 3-Methyl NO NO YES NO NO NO NO YES NO Glucose Xylitol NO NO YESNO NO NO NO NO YES β-Hydroxy YES NO NO NO NO YES NO YES NO butyric acidSebacic acid YES NO NO NO NO NO NO NO NO Hydroxy-L- YES NO YES NO NO YESNO NO YES Proline Putrescine YES NO NO NO NO YES NO NO NO Inulin YES YESYES YES YES YES NO NO NO 2-Deoxy-D- NO NO YES NO NO NO NO YES NO Riboseβ-Methyl-D- NO NO YES NO NO NO NO NO YES Glucuronic acid N-Acetyl-D- NONO NO NO NO NO NO NO NO glucosaminitol γ-Hydroxy YES NO NO NO NO NO NONO NO butyric acid Sorbic acid NO NO NO NO NO NO NO NO NO L-IsoleucineYES NO YES YES NO NO NO YES NO Dihydroxy NO NO YES NO NO YES NO YES NOacetone Laminarin NO YES YES NO NO NO NO NO NO i-Erythritol NO NO NO NONO NO NO NO NO a-Methyl-D- NO NO NO NO NO NO NO NO YES Mannoside γ-aminobutyric YES NO NO YES YES NO NO NO NO acid a-Keto-valeric YES NO NO NONO NO NO NO NO acid Succinamic acid NO NO NO NO NO NO NO NO NO L-LeucineNO NO YES YES NO NO NO NO NO 2,3-Butanediol YES NO NO NO NO NO NO NO NOMannan NO NO NO NO NO NO NO NO NO D-Fucose NO NO NO NO NO NO NO NO NOβ-Methyl-D- NO YES YES NO NO NO NO NO NO Xyloside d-amino valeric YES NONO NO NO NO NO NO NO acid Itaconic acid YES NO YES NO NO YES NO YES NOD-Tartaric acid NO NO NO NO NO NO NO NO NO L-Lysine YES NO NO NO NO NONO NO NO 2,3-Butanone NO NO NO NO NO NO NO NO NO Pectin NO YES YES NO NONO NO YES NO 3-0-β-D- NO NO YES NO NO NO NO NO NO Galacto- pyranosyl-D-arabinose Palatinose NO YES YES NO NO NO NO NO YES Butyric acid YES NONO YES NO NO NO NO NO 5-Keto-D- NO NO NO NO YES NO NO YES NO Gluconicacid L-Tartaric acid NO NO NO NO YES NO NO YES NO L-Methionine NO NO NONO NO NO NO NO NO 3-Hydroxy 2- NO NO NO NO NO NO NO NO NO ButanoneStrain/Substrate SYM00053 SYM00538A SYM00538B SYM00538i SYM00543SYM00563 SYM00574 N-acetyl-D- YES NO NO NO NO NO NO GalactosamineGentiobiose YES NO YES YES NO YES NO D-Raffinose YES NO YES NO NO NO NOCapric acid NO NO NO NO NO NO NO D-lactic acid YES NO NO NO NO NO NOmethyl ester Acetamide NO NO NO NO NO NO YES L-Ornithine NO NO NO NO NONO NO Chondrointin NO NO NO NO NO NO NO sulfate C N-acetyl- NO NO NO NONO NO NO neuraminic acid L-glucose NO NO NO NO NO NO NO Salicin YES NOYES YES NO YES NO Caproic acid NO NO NO NO NO NO NO Malonic acid NO NONO NO NO NO NO L-Alaninamide NO YES NO YES NO NO YES L-Phenylalanine NONO NO NO NO NO YES a-Cyclodextrin NO YES NO NO YES NO NO β-D-allose NONO NO NO NO NO NO Lactitol NO NO YES NO NO NO NO Sedoheptulosan NO NO NONO NO NO NO Citraconic acid NO NO NO NO NO NO YES Melibionic acid YES NONO NO NO NO NO N-Acetyl-L- YES NO NO YES NO NO NO Glutamic acidL-Pyroglutamic NO YES NO YES YES NO YES acid β-Cyclodextrin NO YES YESNO NO NO NO Amygdalin NO NO YES YES NO YES NO D-Melezitose NO NO YES NONO NO NO L-Sorbose NO NO NO NO NO NO NO Citramalic acid NO NO NO NO NONO NO Oxalic acid NO NO NO NO NO NO NO L-Arginine NO NO NO NO YES NO YESL-Valine NO NO NO NO NO NO NO γ-Cyclodextrin NO YES YES NO NO NO NOD-arabinose NO NO NO NO NO NO YES Maltitol NO NO YES NO NO NO NOStachyose NO NO YES NO NO NO NO D-Glucosamine YES YES YES YES YES YESYES Oxalomalic acid NO YES YES YES YES YES YES Glycine NO NO NO NO NO NONO D,L-Carnitine NO NO NO NO NO NO YES Dextrin NO YES YES NO YES NO NOD-arabitol NO NO NO NO NO NO NO a-Methyl-D- NO NO YES NO NO NO NOGlucoside D-Tagatose NO NO NO NO NO NO NO 2-Hydroxy NO NO NO NO NO NO NObenzoic acid Quinic acid NO NO NO NO NO NO NO L-Histidine NO NO NO NOYES NO YES Sec-Butylamine NO NO NO NO NO NO NO Gelatin NO YES NO YES YESNO NO L-arabitol NO NO NO NO NO NO NO β-Methyl-D- NO NO YES NO NO NO YESGalactoside Turanose NO NO YES NO NO NO NO 4-Hydroxy NO NO NO NO NO NOYES benzoic acid D-Ribono-1,4- NO NO NO NO NO NO YES LactoneL-Homoserine NO NO NO NO NO NO YES D,L-Octopamine NO NO NO NO NO NO NOGlycogen NO NO YES NO YES NO NO Arbutin YES YES NO YES NO YES NO3-Methyl NO NO NO NO NO NO NO Glucose Xylitol NO NO NO NO NO NO YESβ-Hydroxy YES NO NO NO NO NO YES butyric acid Sebacic acid NO NO NO NONO NO YES Hydroxy-L- YES NO NO NO YES NO YES Proline Putrescine YES NONO NO NO NO NO Inulin NO YES YES YES NO NO YES 2-Deoxy-D- NO NO NO NO NONO NO Ribose β-Methyl-D- NO NO NO NO NO NO NO Glucuronic acidN-Acetyl-D- NO NO NO NO NO NO NO glucosaminitol γ-Hydroxy NO NO NO NO NONO NO butyric acid Sorbic acid NO NO NO NO NO NO NO L-Isoleucine NO NONO NO NO NO NO Dihydroxy YES NO NO NO NO NO YES acetone Laminarin NO NOYES NO NO NO YES i-Erythritol NO NO NO NO NO NO NO a-Methyl-D- NO NO NONO NO NO NO Mannoside γ-amino butyric NO NO NO NO NO NO YES acida-Keto-valeric NO NO NO NO NO NO NO acid Succinamic acid NO NO NO NO NONO NO L-Leucine NO NO NO NO NO NO NO 2,3-Butanediol NO NO YES NO NO NONO Mannan NO NO NO NO NO NO NO D-Fucose NO NO NO NO NO NO NO β-Methyl-D-NO NO YES NO NO NO NO Xyloside d-amino valeric NO NO NO NO NO NO NO acidItaconic acid YES NO NO NO NO NO NO D-Tartaric acid NO NO NO NO NO NOYES L-Lysine NO NO NO NO NO NO NO 2,3-Butanone NO NO NO NO NO NO NOPectin NO NO YES NO NO NO NO 3-0-β-D- NO NO YES NO NO NO NO Galacto-pyranosyl- D-arabinose Palatinose NO NO YES NO NO NO NO Butyric acid NONO NO NO NO NO NO 5-Keto-D- NO NO NO NO NO NO YES Gluconic acidL-Tartaric acid NO NO NO NO NO NO YES L-Methionine NO NO NO NO NO NO NO3-Hydroxy 2- NO NO NO NO NO NO NO Butanone

TABLE O Substrate utilization as determined by BIOLOG PM2A MicroPlatesby bacterial endophytes belonging to core OTUs. Strain/SubstrateSYM00057B SYM00617 SYM00620 SYM00627 SYM00628 SYM00062C SYM00650SYM00068 N-acetyl-D- NO NO NO NO YES NO NO NO Galactosamine GentiobioseNO YES YES YES YES YES NO NO D-Raffinose NO NO YES YES YES YES NO NOCapric acid NO NO NO NO NO NO NO NO D-lactic acid NO NO NO NO NO NO NONO methyl ester Acetamide NO NO NO NO NO NO NO YES L-Ornithine NO NO NONO NO NO NO YES Chondrointin NO NO NO NO NO NO NO NO sulfate C N-acetyl-NO NO YES NO NO NO NO NO neuraminic acid L-glucose NO NO NO NO NO NO NONO Salicin NO YES NO YES YES YES NO NO Caproic acid NO NO NO NO NO NO NONO Malonic acid NO NO NO NO NO NO NO NO L-Alaninamide NO NO NO NO NO NONO NO L-Phenylalanine NO NO NO NO NO NO NO YES a-Cyclodextrin NO NO NONO NO NO NO NO β-D-allose NO NO NO NO NO NO NO NO Lactitol NO NO NO NONO YES NO NO Sedoheptulosan NO NO NO NO NO NO NO NO Citraconic acid NONO NO NO NO NO NO YES Melibionic acid NO NO YES YES YES NO NO YESN-Acetyl-L- NO NO NO NO NO YES NO NO Glutamic acid L-Pyroglutamic NO NONO NO NO YES NO YES acid β-Cyclodextrin NO NO NO NO NO NO NO NOAmygdalin NO YES NO NO NO YES NO NO D-Melezitose NO YES NO NO NO YES NONO L-Sorbose NO NO NO NO NO NO NO NO Citramalic acid NO NO NO NO NO NONO NO Oxalic acid NO NO NO NO NO NO NO NO L-Arginine NO NO NO NO NO NONO NO L-Valine NO NO NO NO NO NO NO YES γ-Cyclodextrin NO NO NO NO NO NONO NO D-arabinose NO NO NO NO YES NO YES NO Maltitol NO NO NO YES YES NONO NO Stachyose NO NO NO NO NO YES NO NO D-Glucosamine YES YES NO YESYES YES NO YES Oxalomalic YES YES NO NO NO YES NO YES acid Glycine NO NONO NO NO NO NO NO D,L-Carnitine NO NO NO NO NO NO NO NO Dextrin NO YESYES NO NO YES NO NO D-arabitol NO NO NO NO NO NO NO NO a-Methly-D- NO NONO YES YES NO NO NO Glucoside D-Tagatose NO NO NO NO NO NO NO NO2-Hydroxy NO NO NO NO NO NO NO NO benzoic acid Quinic acid NO NO NO NONO NO NO NO L-Histidine YES NO YES NO NO NO YES NO Sec-Butylamine NO NONO NO NO NO NO NO Gelatin NO NO NO NO NO NO NO NO L-arabitol NO NO NO NONO NO NO NO β-Methyl-D- NO NO YES YES YES YES NO NO Galactoside TuranoseNO NO NO YES NO YES NO NO 4-Hydroxy NO NO NO NO NO NO NO NO benzoic acidD-Ribono- NO NO NO NO NO NO NO NO 1,4-Lactone L-Homoserine YES NO NO NONO NO NO NO D,L- NO YES NO NO NO YES NO YES Octopamine Glycogen NO NO NONO NO NO NO NO Arbutin NO YES NO YES YES YES NO NO 3-Methyl NO NO NO NOYES NO NO NO Glucose Xylitol YES NO NO NO NO NO NO NO β-Hydroxy NO NO NONO NO NO NO NO butyric acid Sebacic acid YES NO NO NO NO NO NO NOHydroxy-L- NO NO NO NO NO NO YES NO Proline Putrescine NO NO NO NO YESNO NO NO Inulin YES NO NO NO NO YES NO NO 2-Deoxy-D- NO NO YES NO NO NOYES NO Ribose β-Methyl-D- NO NO NO NO NO NO NO NO Glucuronic acidN-Acetyl-D- NO NO NO NO NO NO NO NO glucosaminitol γ-Hydroxy NO NO NO NONO NO NO NO butyric acid Sorbic acid NO NO NO NO NO NO NO NOL-Isoleucine NO NO NO NO NO YES NO YES Dihydroxy YES NO NO YES YES NOYES NO acetone Laminarin NO NO NO NO NO NO NO NO i-Erythritol NO NO NONO NO NO NO NO a-Methyl-D- NO NO NO NO NO NO NO NO Mannoside γ-amino YESNO NO NO NO NO YES NO butyric acid a-Keto- NO NO NO NO NO NO NO NOvaleric acid Succinamic NO NO NO NO NO NO NO NO acid L-Leucine YES NO NONO NO NO NO NO 2,3-Butanediol NO NO NO NO NO YES NO NO Mannan NO NO NONO NO NO NO NO D-Fucose NO NO NO NO NO NO NO NO β-Methyl- NO NO NO NO NOYES NO NO D-Xyloside d-amino NO NO NO NO NO NO NO NO valeric acidItaconic acid NO NO NO NO NO NO NO NO D-Tartaric acid YES NO NO NO NO NONO NO L-Lysine NO NO NO NO NO NO NO NO 2,3-Butanone NO NO NO NO NO NO NONO Pectin NO NO NO NO NO NO NO NO 3-0-β-D- NO NO NO NO YES NO NO NOGalacto- pyranosyl- D-Arabinose Palatinose NO NO NO YES YES YES NO NOButyric acid NO NO NO NO NO NO NO NO 5-Keto-D- NO NO NO NO NO NO NO NOGluconic acid L-Tartaric acid NO NO NO NO NO NO NO NO L-Methionine NO NONO NO NO NO NO NO 3-Hydroxy NO NO NO NO NO NO NO NO 2-ButanoneStrain/Substrate SYM00070 SYM00714 SYM00009 SYM00905 SYM00924 SYM00963N-acetyl-D- NO YES NO YES NO NO Galactosamine Gentiobiose NO YES NO YESNO NO D-Raffinose NO YES NO NO NO NO Capric acid NO NO NO NO NO NOD-lactic acid NO NO NO NO NO NO methyl ester Acetamide NO NO NO NO NO NOL-Ornithine YES NO YES NO NO NO Chondrointin NO NO NO NO NO NO sulfate CN-acetyl- NO NO NO NO NO NO neuraminic acid L-glucose NO NO NO NO NO NOSalicin NO YES NO YES NO NO Caproic acid NO NO NO NO NO NO Malonic acidNO NO NO NO NO NO L-Alaninamide NO YES NO YES YES NO L-Phenylalanine NONO YES NO NO NO a-Cyclodextrin NO NO NO NO NO NO β-D-allose NO YES NO NONO NO Lactitol NO YES NO YES NO NO Sedoheptulosan NO NO NO NO NO NOCitraconic acid NO NO YES NO YES NO Melibionic acid NO YES NO NO NO NON-Acetyl-L- NO NO NO NO NO NO Glutamic acid L-Pyroglutamic YES YES YESNO NO NO acid β-Cyclodextrin NO NO NO NO NO NO Amygdalin NO NO NO NO NONO D-Melezitose NO YES NO NO NO YES L-Sorbose NO NO NO NO NO YESCitramalic acid NO NO NO NO NO NO Oxalic acid NO NO NO NO NO NOL-Arginine NO YES NO NO NO NO L-Valine YES YES YES NO NO NOγ-Cyclodextrin NO NO NO NO NO NO D-arabinose NO YES NO NO YES YESMaltitol NO YES NO YES NO YES Stachyose NO NO NO NO NO YES D-GlucosamineYES YES YES YES NO NO Oxalomalic YES YES YES YES NO NO acid Glycine NONO NO NO NO NO D,L-Carnitine YES NO YES NO NO NO Dextrin NO NO NO NO NONO D-arabitol NO NO NO NO NO NO a-Methly-D- NO YES NO NO NO YESGlucoside D-Tagatose NO NO NO NO NO NO 2-Hydroxy NO NO NO NO NO NObenzoic acid Quinic acid NO NO NO NO NO NO L-Histidine YES YES NO NO NONO Sec-Butylamine NO NO NO NO NO NO Gelatin NO NO NO YES NO NOL-arabitol NO NO NO NO NO NO β-Methyl-D- NO YES NO NO NO YES GalactosideTuranose NO YES NO NO NO YES 4-Hydroxy NO NO NO NO NO NO benzoic acidD-Ribono- NO YES NO NO NO NO 1,4-Lactone L-Homoserine NO NO NO NO NO NOD,L- YES NO YES YES NO YES Octopamine Glycogen NO NO NO NO NO NO ArbutinYES YES NO YES NO NO 3-Methyl NO NO NO NO NO NO Glucose Xylitol YES YESYES NO NO NO β-Hydroxy NO NO NO NO NO NO butyric acid Sebacic acid NO NONO NO NO NO Hydroxy-L- NO NO NO NO NO NO Proline Putrescine YES NO NO NONO NO Inulin NO NO NO NO NO NO 2-Deoxy-D- NO NO NO NO YES NO Riboseβ-Methyl-D- NO NO NO NO NO NO Glucuronic acid N-Acetyl-D- NO NO NO NO NONO glucosaminitol γ-Hydroxy NO NO NO NO YES NO butyric acid Sorbic acidNO NO NO NO NO NO L-Isoleucine YES YES YES NO NO NO Dihydroxy NO NO NONO YES YES acetone Laminarin NO NO NO NO NO NO i-Erythritol NO NO NO NONO NO a-Methyl-D- NO NO NO NO NO NO Mannoside γ-amino YES YES NO NO NONO butyric acid a-Keto- NO NO NO NO NO NO valeric acid Succinamic NO NONO NO YES NO acid L-Leucine NO YES YES NO NO NO 2,3-Butanediol NO NO NONO NO NO Mannan NO NO NO NO NO NO D-Fucose NO YES NO NO NO NO β-Methyl-NO YES NO NO NO NO D-Xyloside d-amino NO NO NO NO NO NO valeric acidItaconic acid NO NO NO NO NO NO D-Tartaric acid NO NO NO NO NO NOL-Lysine NO NO NO NO NO NO 2,3-Butanone NO NO NO NO NO NO Pectin NO NONO NO NO NO 3-0-β-D- NO NO NO NO NO NO Galacto- pyranosyl- D-ArabinosePalatinose NO YES NO YES NO YES Butyric acid NO NO NO NO NO NO 5-Keto-D-NO NO NO NO NO NO Gluconic acid L-Tartaric acid YES NO YES NO NO NOL-Methionine NO NO NO NO NO NO 3-Hydroxy NO NO NO NO NO NO 2-ButanoneStrain/Substrate SYM00978 SYM00982 SYM00987 SYM00991 SYM00999N-acetyl-D- NO NO NO YES NO Galactosamine Gentiobiose NO NO NO NO NOD-Raffinose NO NO NO YES NO Capric acid NO NO NO NO NO D-lactic acid NONO NO NO NO methyl ester Acetamide NO NO NO NO NO L-Ornithine NO NO NONO NO Chondrointin NO NO NO NO NO sulfate C N-acetyl- NO NO NO NO NOneuraminic acid L-glucose NO NO NO NO NO Salicin NO NO NO YES NO Caproicacid NO NO NO NO NO Malonic acid NO NO NO NO NO L-Alaninamide NO NO NONO NO L-Phenylalanine NO NO NO NO NO a-Cyclodextrin NO YES NO NO NOβ-D-allose NO NO NO NO NO Lactitol NO NO NO NO NO Sedoheptulosan NO NONO NO NO Citraconic acid NO NO NO NO NO Melibionic acid YES NO NO NO NON-Acetyl-L- NO NO YES NO NO Glutamic acid L-Pyroglutamic NO YES YES NONO acid β-Cyclodextrin NO YES NO NO NO Amygdalin NO NO NO YES NOD-Melezitose NO NO YES NO NO L-Sorbose NO NO YES NO NO Citramalic acidNO NO NO NO NO Oxalic acid NO NO NO NO NO L-Arginine NO NO NO NO NOL-Valine NO NO NO NO NO γ-Cyclodextrin NO NO NO NO NO D-arabinose NO NONO NO NO Maltitol NO NO NO NO NO Stachyose NO NO NO NO NO D-GlucosamineYES NO YES YES YES Oxalomalic YES NO YES NO YES acid Glycine NO NO NO NONO D,L-Carnitine NO NO NO NO NO Dextrin NO NO NO YES NO D-arabitol NO NONO NO NO a-Methly-D- NO NO NO NO NO Glucoside D-Tagatose NO NO NO NO NO2-Hydroxy NO NO NO NO NO benzoic acid Quinic acid NO NO NO NO NOL-Histidine NO NO NO NO NO Sec-Butylamine NO NO NO NO NO Gelatin NO YESNO NO NO L-arabitol NO NO NO NO NO β-Methyl-D- YES NO YES NO NOGalactoside Turanose NO NO YES NO NO 4-Hydroxy NO NO NO NO NO benzoicacid D-Ribono- NO NO NO NO NO 1,4-Lactone L-Homoserine NO NO NO NO NOD,L- NO NO YES YES NO Octopamine Glycogen NO NO NO NO NO Arbutin YES NONO YES NO 3-Methyl NO NO NO NO NO Glucose Xylitol NO NO NO NO NOβ-Hydroxy NO NO NO NO NO butyric acid Sebacic acid YES NO NO NO NOHydroxy-L- NO NO YES YES YES Proline Putrescine NO NO NO NO NO Inulin NONO YES NO YES 2-Deoxy-D- NO NO NO NO NO Ribose β-Methyl-D- NO NO NO NONO Glucuronic acid N-Acetyl-D- NO NO NO NO NO glucosaminitol γ-HydroxyNO NO NO NO NO butyric acid Sorbic acid NO NO NO NO NO L-Isoleucine NONO NO NO NO Dihydroxy NO NO YES NO NO acetone Laminarin NO YES NO NO NOi-Erythritol NO NO NO NO NO a-Methyl-D- NO NO NO NO NO Mannoside γ-aminoNO NO NO NO NO butyric acid a-Keto- NO NO NO NO NO valeric acidSuccinamic NO NO NO NO NO acid L-Leucine NO NO NO NO NO 2,3-ButanediolNO NO NO NO NO Mannan NO NO NO NO NO D-Fucose NO NO NO NO NO β-Methyl-NO NO NO NO NO D-Xyloside d-amino NO NO NO NO NO valeric acid Itaconicacid NO NO NO YES NO D-Tartaric acid NO NO NO NO NO L-Lysine NO NO NO NONO 2,3-Butanone NO NO NO NO NO Pectin NO NO NO YES NO 3-0-β-D- NO NO YESNO NO Galacto- pyranosyl- D-Arabinose Palatinose YES NO YES NO NOButyric acid NO NO NO NO NO 5-Keto-D- NO NO NO NO NO Gluconic acidL-Tartaric acid NO NO NO NO NO L-Methionine NO NO NO NO NO 3-Hydroxy NONO NO NO NO 2-Butanone

TABLE P Substrate utilization as determined by BIOLOG PM1 MicroPlates byfungal endophytes belonging to core OTUs. Strain/Substrate SYM00120SYM00122 SYM00123 SYM00124 SYM00129 SYM01300 SYM01310 SYM01311 SYM01314D-Serine NO NO YES YES NO NO NO YES NO D-Glucose-6- NO NO NO YES YES NONO NO YES Phosphate L-Asparagine NO NO NO YES NO YES YES YES YESL-glutamine NO NO NO YES YES YES YES YES YES Glycyl-L- NO NO NO NO NOYES NO YES NO Aspartic acid Glycyl-L- NO NO NO YES NO YES YES YES YESGlutamic acid Glycyl-L- NO NO NO YES NO YES NO YES YES ProlineL-Arabinose YES NO NO NO YES NO YES YES YES D-Sorbitol NO NO YES YES YESYES YES YES YES D-Galactonic NO NO NO NO NO YES NO NO YES acid-?-lactoneD-Aspartic acid NO NO YES YES NO NO NO YES NO m-Tartaric acid NO NO NOYES NO YES NO YES YES Citric acid NO NO NO YES NO YES YES YES YESTricarballylic NO NO NO YES NO YES NO YES YES acid p-Hydroxy NO NO NOYES NO NO NO NO YES Phenyl acetic acid N-Acetyl-D- NO NO YES YES YES YESYES YES YES Glucosamine Glycerol YES NO NO YES YES YES YES YES NOD-L-Malic acid NO NO NO YES NO YES YES YES YES D-Glucos- NO NO NO YES NOYES NO NO YES aminic acid D-Glucose-1- NO NO YES YES NO YES NO NO YESPhosphate m-Inositol NO NO NO YES NO YES YES YES YES L-Serine NO NO NOYES NO YES YES YES YES m-Hydroxy NO NO NO YES NO YES NO NO NO PhenylAcetic acid D-Saccharic NO NO NO YES NO YES YES YES YES acid L-Fucose NONO NO YES NO YES NO YES YES D-Ribose NO NO YES YES YES YES YES YES NO1,2-Propanediol NO NO NO YES NO NO NO NO NO D-Fructose-6- NO NO NO NO NONO NO NO NO Phosphate D-Threonine NO NO YES YES NO NO NO YES NOL-Threonine NO YES NO YES NO YES NO YES NO Tyramine YES NO NO YES NO YESYES YES YES Succinic acid NO NO NO YES NO YES YES YES NO D-Glucuronic NONO YES YES YES YES YES YES YES acid Tween 20 NO NO NO YES YES YES YESYES YES Tween 40 NO NO YES YES YES YES NO YES YES Tween 80 NO NO YES NOYES YES YES YES YES Fumaric acid NO NO YES NO NO YES YES YES YESL-Alanine NO NO NO YES NO YES YES YES YES D-Psicose NO NO NO YES NO NONO NO NO D-Galactose YES NO YES YES NO YES YES YES YES D-Gluconic NO NONO YES YES YES YES YES YES acid L-Rhamnose NO NO NO YES YES YES NO YESYES a-Keto-Glutaric NO NO NO YES NO YES YES YES YES acid a-Hydroxy NO NOYES YES NO YES YES YES YES Glutaric acid-?-lactone Bromo succinic NO NOYES YES NO YES YES YES YES acid L-Alanyl- NO NO YES YES NO YES YES YESYES Glycine L-Lyxose NO NO NO YES NO NO NO NO NO L-Aspartic acid NO NOYES YES NO YES YES YES YES D-L-a-Glycerol NO NO NO YES NO NO YES NO YESphosphate D-Fructose NO NO NO YES YES YES YES YES YES a-Keto-Butyric NONO NO YES NO NO NO YES NO acid a-Hydroxy NO NO NO YES NO NO NO YES NOButyric acid Propionic acid NO NO YES YES NO YES YES YES YES AcetoaceticNO NO NO YES NO NO NO NO NO acid Glucuronamide NO NO NO NO NO NO NO NONO L-Proline NO NO NO YES NO YES YES YES YES D-Xylose YES NO NO YES YESYES YES YES YES Acetic acid NO NO YES YES NO NO NO YES NO a-Methyl-D- NONO NO YES YES NO YES YES NO Galactoside β-Methyl-D- NO NO YES YES YESYES YES YES YES glucoside Mucic acid NO NO NO YES YES YES YES YES YESN-acetyl-β-D- NO NO YES YES NO NO NO NO NO Mannosamine Pyruvic acid NONO YES YES YES YES YES YES YES D-Alanine NO NO YES YES NO YES YES YESYES L-Lactic acid NO NO YES NO NO YES YES YES YES a-D-Glucose NO NO NOYES YES YES YES YES YES a-D-Lactose NO NO YES YES YES YES NO YES YESAdonitol NO NO NO YES NO YES YES YES YES Glycolic acid NO NO YES YES NONO NO NO NO Mono Methyl NO NO NO YES NO YES NO YES YES SuccinateL-Galactonic- NO NO NO NO NO YES YES YES YES acid-?-lactone D-TrehaloseNO NO NO YES YES YES YES YES YES Formic acid NO NO NO YES NO NO NO NO NOMaltose YES NO YES YES YES YES YES YES YES Lactulose YES NO NO YES NOYES NO YES NO Maltotriose NO NO YES YES YES YES NO YES YES Glyoxylicacid NO NO YES YES NO NO NO NO NO Methyl NO NO YES YES NO YES YES YES NOPyruvate D-Galacturonic NO NO YES YES YES YES YES YES YES acid D-MannoseNO NO YES YES YES YES YES YES YES D-Mannitol NO NO YES YES YES YES YESYES YES D-Melibiose NO NO YES YES YES YES YES YES NO Sucrose NO NO YESYES YES YES YES YES YES 2-Deoxy NO NO NO NO NO NO NO YES NO adenosineD-Cellobiose NO NO YES YES NO YES YES YES YES D-Malic acid NO NO NO YESNO YES YES YES YES Phenylethyl- NO NO NO NO NO NO NO NO NO amineDulcitol NO NO YES YES YES YES NO YES NO L-Glutamic NO NO YES YES NO YESYES YES YES acid Thymidine NO NO NO YES NO NO NO NO NO Uridine NO NO YESYES NO YES YES YES YES Adenosine NO NO YES YES NO YES NO NO YES InosineNO NO NO YES YES YES YES YES YES L-Malic acid YES NO NO YES NO YES YESYES YES 2-Amino- NO NO YES YES NO YES YES YES YES ethanolStrain/Substrate SYM01315 SYM01325 SYM01326 SYM01327 SYM01328 SYM01333SYM0135 SYM0136 D-Serine YES NO NO NO NO NO NO NO D-Glucose-6- NO NO NOYES YES NO NO NO Phosphate L-Asparagine NO YES YES YES YES YES NO NOL-glutamine NO YES YES YES NO YES YES NO Glycyl-L- YES NO YES n/a NO NONO NO Aspartic acid Glycyl-L- YES NO NO YES YES NO NO NO Glutamic acidGlycyl-L- NO NO YES YES YES NO NO NO Proline L-Arabinose YES YES YES YESYES YES YES YES D-Sorbitol YES YES YES YES YES YES YES YES D-GalactonicNO NO NO YES NO YES NO NO acid-?-lactone D-Aspartic acid NO NO NO NO NONO NO NO m-Tartaric acid YES NO NO NO NO NO NO NO Citric acid YES NO YESn/a NO YES NO NO Tricarballylic NO YES NO YES YES NO YES NO acidp-Hydroxy NO NO YES YES NO NO NO NO Phenyl acetic acid N-Acetyl-D- YESYES YES YES NO YES YES YES Glucosamine Glycerol YES YES NO YES YES YESNO NO D-L-Malic acid YES NO NO YES YES YES NO NO D-Glucos- NO NO YES YESNO NO NO NO aminic acid D-Glucose-1- NO NO NO YES NO NO NO NO Phosphatem-Inositol YES YES YES n/a NO YES NO NO L-Serine NO NO YES YES NO YES NONO m-Hydroxy YES NO NO NO YES NO NO NO Phenyl Acetic acid D-SaccharicYES YES YES YES NO YES NO NO acid L-Fucose YES NO NO YES NO NO NO NOD-Ribose YES YES YES YES YES NO YES NO 1,2-Propanediol NO NO NO NO NO NONO NO D-Fructose-6- NO NO NO NO NO NO NO NO Phosphate D-Threonine NO NONO n/a YES NO NO NO L-Threonine NO NO YES NO YES NO NO NO Tyramine YESNO YES YES NO YES NO NO Succinic acid NO NO YES YES NO YES NO NOD-Glucuronic YES NO YES YES YES YES YES NO acid Tween 20 YES NO YES YESNO YES YES YES Tween 40 YES YES YES YES YES YES YES YES Tween 80 YES YESYES YES YES YES YES YES Fumaric acid YES YES YES n/a YES YES NO NOL-Alanine YES YES YES YES YES YES NO NO D-Psicose NO NO NO NO YES NO NONO D-Galactose YES YES YES YES YES YES YES YES D-Gluconic NO YES YES YESYES YES YES YES acid L-Rhamnose YES YES NO YES NO NO NO NOa-Keto-Glutaric NO NO YES YES YES YES NO NO acid a-Hydroxy NO NO NO YESYES YES NO NO Glutaric acid-?-lactone Bromo succinic NO YES YES n/a NONO NO NO acid L-Alanyl- NO NO YES YES YES YES NO NO Glycine L-Lyxose NONO NO NO NO NO NO NO L-Aspartic acid YES NO YES YES YES YES NO NOD-L-a-Glycerol YES NO NO YES NO NO NO NO phosphate D-Fructose YES YESYES YES YES YES YES NO a-Keto-Butyric YES NO NO YES NO NO NO NO acida-Hydroxy NO NO NO NO NO NO NO NO Butyric acid Propionic acid NO NO NOn/a NO NO NO NO Acetoacetic YES NO NO NO NO NO NO NO acid GlucuronamideNO NO NO NO NO NO NO NO L-Proline YES YES NO YES YES YES YES NO D-XyloseNO YES NO YES NO YES YES NO Acetic acid NO NO NO YES NO NO NO NOa-Methyl-D- NO YES YES YES YES NO YES YES Galactoside β-Methyl-D- NO YESYES NO YES NO YES YES glucoside Mucic acid YES NO YES n/a YES YES NO NON-acetyl-β-D- YES NO NO NO YES NO NO NO Mannosamine Pyruvic acid NO NOYES YES NO YES NO NO D-Alanine NO NO YES YES NO YES NO NO L-Lactic acidYES NO YES YES NO YES NO NO a-D-Glucose YES YES YES YES YES YES YES YESa-D-Lactose NO NO YES YES YES YES NO NO Adonitol YES YES NO YES NO YESNO NO Glycolic acid NO NO NO n/a NO NO NO NO Mono Methyl NO NO NO YES NONO NO NO Succinate L-Galactonic- NO YES YES YES NO YES YES NOacid-?-lactone D-Trehalose YES YES YES YES NO YES YES NO Formic acid YESNO NO NO YES NO NO NO Maltose NO YES YES YES YES YES YES YES LactuloseYES NO NO YES YES NO NO NO Maltotriose YES YES YES YES YES NO YES YESGlyoxylic acid NO NO NO n/a NO NO NO NO Methyl NO NO YES YES NO NO NO NOPyruvate D-Galacturonic NO NO YES YES NO YES NO NO acid D-Mannose NO YESYES YES YES YES YES YES D-Mannitol YES YES YES YES NO YES YES YESD-Melibiose NO YES NO YES YES NO YES YES Sucrose NO YES YES YES YES YESYES YES 2-Deoxy NO NO NO NO NO NO NO NO adenosine D-Cellobiose NO YESYES n/a YES NO YES NO D-Malic acid NO NO NO YES NO NO NO NO Phenylethyl-NO NO NO NO NO NO NO NO amine Dulcitol NO NO NO NO YES NO NO NOL-Glutamic YES YES YES YES NO YES YES YES acid Thymidine NO NO NO YESYES NO NO NO Uridine NO NO YES YES NO YES NO YES Adenosine YES NO NO YESNO YES NO NO Inosine YES NO YES n/a NO YES NO NO L-Malic acid YES YESYES YES NO YES NO NO 2-Amino- NO YES NO YES NO YES NO NO ethanol

TABLE Q Substrate utilization as determined by BIOLOG PM1 MicroPlates byfungal endophytes belonging to core OTUs. Strain/Substrate SYM00151SYM00154 SYM015811 SYM15820 SYM15825 SYM15828 SYM15831 SYM15837 SYM15839D-Serine NO NO NO NO YES NO NO NO YES D-Glucose-6- YES YES NO NO NO NONO NO NO Phosphate L-Asparagine YES NO YES YES YES YES YES YES NOL-glutamine YES NO NO YES YES YES YES YES YES Glycyl-L- NO YES YES YESYES YES NO NO NO Aspartic acid Glycyl-L- NO YES NO YES YES YES NO YES NOGlutamic acid Glycyl-L-Proline YES YES NO YES YES YES YES NO NOL-Arabinose YES YES NO YES YES YES YES YES YES D-Sorbitol YES YES YESYES YES YES YES YES YES D-Galactonic NO YES YES YES NO NO NO YES YESacid-?-lactone D-Aspartic acid NO YES NO NO NO NO NO YES NO m-Tartaricacid YES NO NO NO YES NO YES NO YES Citric acid YES YES YES YES YES YESYES YES NO Tricarballylic acid YES NO NO NO YES NO NO YES YES p-HydroxyPhenyl YES YES YES YES NO YES NO YES YES acetic acid N-Acetyl-D- YES YESNO YES YES YES YES NO YES Glucosamine Glycerol YES YES YES YES YES YESYES NO YES D-L-Malic acid NO YES NO YES YES YES NO YES YESD-Glucosaminic NO YES YES NO NO NO NO NO NO acid D-Glucose-1- NO NO NONO NO NO NO NO NO Phosphate m-Inositol YES YES NO YES YES YES NO YES YESL-Serine NO NO NO YES YES YES NO YES NO m-Hydroxy Phenyl NO NO NO NO NONO NO NO NO Acetic acid D-Saccharic acid YES NO NO YES YES YES YES YESYES L-Fucose NO YES NO NO NO YES YES NO NO D-Ribose YES YES NO YES YESYES YES YES YES 1,2-Propanediol NO YES NO NO NO YES NO NO NOD-Fructose-6- NO YES NO NO NO NO NO NO NO Phosphate D-Threonine NO NO NONO NO NO NO YES NO L-Threonine NO NO YES YES YES NO NO YES NO TyramineYES YES NO NO YES YES NO YES YES Succinic acid YES YES NO YES YES YES NOYES NO D-Glucuronic acid NO YES NO YES YES YES NO NO NO Tween 20 YES YESYES YES YES YES YES YES YES Tween 40 YES YES YES YES YES YES YES YES YESTween 80 YES YES NO YES YES YES YES YES YES Fumaric acid NO NO YES YESYES YES YES NO NO L-Alanine YES NO YES YES YES YES YES NO NO D-PsicoseNO YES NO NO NO NO NO NO NO D-Galactose YES YES NO YES YES YES YES YESYES D-Gluconic acid YES YES YES YES YES YES YES YES YES L-Rhamnose YESYES NO NO YES NO NO YES YES a-Keto-Glutaric acid NO NO YES YES NO YES NONO NO a-Hydroxy Glutaric NO YES NO YES NO YES NO YES NO acid-?-lactoneBromo succinic acid NO YES NO NO YES YES NO NO YES L-Alanyl-Glycine YESYES YES YES YES YES YES YES YES L-Lyxose NO NO NO NO NO NO NO NO NOL-Aspartic acid YES NO NO YES YES YES YES YES NO D-L-a-Glycerol NO YESYES YES NO YES NO YES YES phosphate D-Fructose YES YES YES YES YES YESYES YES YES a-Keto-Butyric acid NO YES NO NO YES NO NO NO NO a-HydroxyNO YES NO NO YES NO NO NO NO Butyric acid Propionic acid NO YES NO NOYES YES YES YES YES Acetoacetic acid NO NO NO NO NO NO NO NO NOGlucuronamide NO NO YES NO NO NO NO YES NO L-Proline YES YES NO YES YESYES YES YES YES D-Xylose YES NO NO YES YES YES YES YES YES Acetic acidYES YES NO YES YES YES YES YES YES a-Methyl-D- YES NO NO NO YES YES YESYES YES Galactoside β-Methyl-D- YES YES NO NO YES NO YES YES YESglucoside Mucic acid YES YES NO YES YES YES YES YES YES N-acetyl-β-D- NOYES NO NO NO YES NO YES NO Mannosamine Pyruvic acid YES YES NO YES YESYES YES NO YES D-Alanine YES NO YES YES NO YES YES YES NO L-Lactic acidYES NO NO YES YES YES YES NO YES a-D-Glucose YES YES YES YES YES YES YESYES YES a-D-Lactose YES NO NO NO YES NO NO YES NO Adonitol YES YES YESYES YES YES NO YES NO Glycolic acid NO YES NO NO YES NO NO NO NO MonoMethyl YES NO NO NO YES NO YES NO NO Succinate L-Galactonic- YES YES NOYES YES YES YES YES YES acid-?-lacone D-Trehalose YES YES NO YES YES YESYES YES YES Formic acid YES NO NO NO YES NO NO NO NO Maltose YES YES NOYES YES NO YES YES YES Lactulose YES YES NO NO YES NO YES YES NOMaltotriose YES NO NO YES YES YES YES YES YES Glyoxylic acid NO YES NONO YES NO NO NO NO Methyl Pyruvate YES NO NO YES YES YES YES YES YESD-Galacturonic acid YES YES YES YES YES YES YES YES YES D-Mannose YESYES NO YES YES YES YES YES YES D-Mannitol YES YES YES YES YES YES YESYES YES D-Melibiose YES NO YES YES YES YES YES YES YES Sucrose YES YESNO YES YES YES YES YES YES 2-Deoxy adenosine YES NO NO NO YES NO NO NOYES D-Cellobiose YES YES NO YES YES NO YES YES YES D-Malic acid YES YESYES NO YES NO NO YES YES Phenylethyl-amine NO NO NO NO NO NO NO NO NODulcitol YES YES NO NO YES NO YES YES YES L-Glutamic acid YES YES YESYES YES YES YES YES YES Thymidine NO YES NO NO YES NO YES NO NO UridineYES YES YES YES YES NO YES YES NO Adenosine NO YES YES YES NO YES YESYES NO Inosine YES NO YES YES NO YES YES YES NO L-Malic acid YES YES NOYES NO YES YES NO NO 2-Aminoethanol YES YES NO YES YES YES NO YES NOStrain/Substrate SYM15847 SYM15872 SYM15890 SYM15901 SYM15920 SYM15926SYM15928 D-Serine YES NO NO NO YES NO NO D-Glucose-6- NO NO NO NO NO NONO Phosphate L-Asparagine YES YES NO YES YES YES YES L-glutamine YES YESYES YES YES NO NO Glycyl-L- NO NO NO NO YES NO NO Aspartic acidGlycyl-L- YES YES YES YES YES NO NO Glutamic acid Glycyl-L-Proline YESYES NO YES YES NO YES L-Arabinose YES YES YES YES YES NO YES D-SorbitolYES YES YES YES YES NO YES D-Galactonic NO NO NO NO YES YES NOacid-?-lactone D-Aspartic acid NO NO NO NO YES NO YES m-Tartaric acid NOYES NO YES YES NO NO Citric acid YES NO YES NO NO NO NO Tricarballylicacid YES YES YES YES YES NO NO p-Hydroxy Phenyl NO NO NO NO YES NO NOacetic acid N-Acetyl-D- YES YES YES YES YES YES YES Glucosamine GlycerolYES YES YES YES YES YES YES D-L-Malic acid NO YES YES YES YES NO NOD-Glucosaminic NO NO YES NO NO NO NO acid D-Glucose-1- NO NO NO NO NO NONO Phosphate m-Inositol YES YES YES YES YES NO NO L-Serine NO YES NO YESYES NO NO m-Hydroxy Phenyl NO NO NO NO NO NO NO Acetic acid D-Saccharicacid NO YES YES YES YES NO YES L-Fucose NO NO NO NO NO NO NO D-RiboseYES YES NO YES YES NO YES 1,2-Propanediol NO NO NO NO NO NO NOD-Fructose-6- NO NO NO NO NO NO NO Phosphate D-Threonine NO NO NO NO YESNO NO L-Threonine NO YES NO YES YES NO NO Tyramine YES YES NO YES YESYES NO Succinic acid NO NO YES YES YES NO NO D-Glucuronic acid YES YESYES YES YES YES YES Tween 20 YES YES NO YES YES YES YES Tween 40 NO YESYES YES YES NO YES Tween 80 YES YES YES YES YES NO YES Fumaric acid NOYES NO YES YES NO YES L-Alanine YES YES YES YES YES YES NO D-Psicose NONO NO NO NO NO NO D-Galactose YES YES NO YES YES YES NO D-Gluconic acidYES YES YES YES YES NO YES L-Rhamnose YES YES NO YES YES NO NOa-Keto-Glutaric acid NO YES YES NO NO NO NO a-Hydroxy Glutaric NO NO NONO NO NO NO acid-?-lactone Bromo succinic acid YES YES NO YES YES NO NOL-Alanyl-Glycine YES YES YES YES YES NO YES L-Lyxose NO NO NO NO YES YESNO L-Aspartic acid YES YES YES YES YES NO YES D-L-a-Glycerol NO YES NONO NO YES NO phosphate D-Fructose YES YES YES YES YES NO NOa-Keto-Butyric acid YES YES NO NO NO NO NO a-Hydroxy NO NO NO NO NO NONO Butyric acid Propionic acid NO NO YES YES YES NO NO Acetoacetic acidNO NO NO NO YES NO NO Glucuronamide NO NO NO NO NO NO NO L-Proline YESYES YES YES YES YES YES D-Xylose YES YES NO YES YES NO YES Acetic acidYES YES NO YES YES YES NO a-Methyl-D- YES YES NO YES YES NO NOGalactoside β-Methyl-D- YES YES NO YES YES NO YES glucoside Mucic acidYES YES YES YES YES NO NO N-acetyl-β-D- NO NO NO NO NO NO NO MannosaminePyruvic acid YES YES YES YES YES NO YES D-Alanine NO NO NO NO YES YES NOL-Lactic acid YES YES NO YES YES NO YES a-D-Glucose YES YES YES YES YESYES YES a-D-Lactose YES YES NO YES YES NO NO Adonitol NO YES NO YES YESNO NO Glycolic acid NO NO NO NO NO NO NO Mono Methyl NO NO YES NO NO NOYES Succinate L-Galactonic- YES YES YES YES YES YES YES acid-?-laconeD-Trehalose YES YES YES YES YES NO YES Formic acid NO YES YES YES NO NONO Maltose YES YES YES YES YES YES YES Lactulose NO YES NO YES YES NO NOMaltotriose YES YES NO YES YES YES YES Glyoxylic acid NO YES NO YES NONO NO Methyl Pyruvate YES YES YES YES YES NO YES D-Galacturonic acid YESYES NO YES YES YES NO D-Mannose YES YES YES YES YES NO YES D-MannitolYES YES NO YES YES NO YES D-Melibiose YES YES NO YES YES NO YES SucroseYES YES YES YES YES NO YES 2-Deoxy adenosine NO YES NO YES NO NO NOD-Cellobiose YES YES YES YES YES NO YES D-Malic acid NO YES NO YES YESNO NO Phenylethyl-amine NO NO NO NO NO NO NO Dulcitol YES YES NO YES YESNO YES L-Glutamic acid YES YES YES YES YES NO NO Thymidine NO YES NO YESNO NO NO Uridine YES YES YES YES NO NO NO Adenosine YES YES NO YES NO NONO Inosine NO NO YES YES YES YES NO L-Malic acid YES YES NO YES YES NOYES 2-Aminoethanol YES YES NO YES YES YES YES

TABLE R Substrate utilization as determined by BIOLOG PM1 MicroPlates byfungal endophytes belonging to core OTUs. Strain/ Substrate SYM15932SYM00160 SYM00034 SYM00566B SYM00577 SYM00590 SYM00603 SYM00061ASYM00622 D-Serine NO NO NO NO NO NO NO YES NO D-Glucose-6- NO NO NO NONO NO NO NO NO Phosphate L-Asparagine NO NO YES NO YES YES YES YES YESL-glutamine NO YES YES YES YES NO YES YES YES Glycyl-L- NO NO YES NO NONO NO YES NO Aspartic acid Glycyl-L- NO NO NO NO NO NO YES YES NOGlutamic acid Glycyl-L- NO YES NO YES YES NO YES YES NO ProlineL-Arabinose YES NO YES NO YES YES YES YES YES D-Sorbitol NO NO YES NOYES YES YES YES YES D-Galactonic NO NO NO YES NO NO YES NO YESacid-?-lactone D-Aspartic acid NO NO NO NO NO NO NO NO NO m-Tartaricacid NO NO NO YES YES NO NO YES NO Citric acid NO NO NO YES YES NO YESYES YES Tricarballylic NO NO NO NO NO NO NO NO NO acid p-Hydroxy NO NONO YES YES NO YES NO NO Phenyl acetic acid N-Acetyl-D- NO NO YES YES YESYES YES YES YES Glucosamine Glycerol NO NO YES YES NO NO YES YES NOD-L-Malic acid NO YES NO NO YES NO YES YES YES D-Glucosaminic NO NO YESYES NO NO YES NO NO acid D-Glucose-1- NO NO NO NO NO NO NO NO NOPhosphate m-Inositol NO NO NO YES YES NO YES YES YES L-Serine NO NO NOYES YES NO YES YES YES m-Hydroxy NO NO NO NO NO NO NO NO NO PhenylAcetic acid D-Saccharic NO NO NO YES YES NO YES YES YES acid L-Fucose NONO NO NO NO NO NO NO NO D-Ribose NO NO YES YES YES YES YES YES YES1,2-Propanediol NO NO NO NO NO NO NO NO NO D-Fructose-6- NO NO NO YES NONO NO NO NO Phosphate D-Threonine NO NO NO NO NO NO NO YES NOL-Threonine NO NO NO NO YES NO NO YES NO Tyramine YES NO NO NO YES NOYES NO YES Succinic acid NO NO YES NO NO NO YES YES YES D-Glucuronic YESNO NO NO YES NO YES YES YES acid Tween 20 NO NO YES NO YES YES YES YESNO Tween 40 NO YES YES YES YES NO YES YES YES Tween 80 NO NO YES YES YESNO YES YES YES Fumaric acid NO YES YES YES NO NO YES YES YES L-AlanineNO NO NO NO YES YES YES YES YES D-Psicose NO NO NO NO NO NO NO YES NOD-Galactose NO NO YES NO YES NO YES YES YES D-Gluconic NO NO NO YES YESYES YES YES YES acid L-Rhamnose NO NO YES NO YES NO NO YES NOa-Keto-Glutaric NO NO YES NO NO NO YES NO NO acid a-Hydroxy NO NO NO YESYES NO YES YES YES Glutaric acid-?-lactone Bromo succinic NO NO YES NONO NO YES YES NO acid L-Alanyl- NO NO NO NO NO NO YES YES YES GlycineL-Lyxose NO YES NO NO NO NO NO YES NO L-Aspartic acid NO NO YES YES YESNO YES YES YES D-L-a-Glycerol NO NO NO YES NO NO YES NO YES phosphateD-Fructose YES YES YES YES YES YES YES YES YES a-Keto-Butyric NO NO NONO NO NO NO YES NO acid a-Hydroxy NO NO NO NO NO NO NO NO NO Butyricacid Propionic acid NO NO NO NO NO NO YES NO NO Acetoacetic NO NO NO NONO NO NO NO NO acid Glucuronamide NO NO NO NO NO NO NO NO NO L-ProlineNO YES YES NO YES NO YES YES YES D-Xylose NO NO NO YES YES NO YES YESYES Acetic acid NO NO NO NO NO NO NO NO NO a-Methyl-D- YES NO NO NO YESNO NO YES NO Galactoside β-Methyl-D- YES YES YES YES YES YES NO YES NOglucoside Mucic acid NO NO NO YES YES NO YES YES YES N-acetyl-β-D- NO NONO NO NO NO NO YES NO Mannosamine Pyruvic acid NO NO NO NO YES NO NO YESNO D-Alanine NO NO NO YES YES NO YES YES YES L-Lactic acid NO NO NO NONO NO YES YES YES a-D-Glucose YES YES YES YES YES YES YES YES YESa-D-Lactose NO NO NO NO NO NO NO YES NO Adonitol NO NO NO NO YES NO YESYES YES Glycolic acid NO NO NO NO NO NO NO NO NO Mono Methyl YES NO NONO YES NO NO YES NO Succinate L-Galactonic- NO NO NO NO YES NO YES YESNO acid-?-lactone D-Trehalose YES NO YES YES YES YES YES YES YES Formicacid NO NO NO NO NO NO NO NO NO Maltose YES YES YES NO YES YES NO YES NOLactulose NO NO NO NO NO NO NO YES NO Maltotriose YES YES YES NO YES YESNO YES NO Glyoxylic acid NO NO NO NO NO NO NO NO NO Methyl NO YES NO NONO NO NO YES NO Pyruvate D-Galacturonic NO NO NO NO YES YES YES YES YESacid D-Mannose YES YES YES YES YES NO YES YES YES D-Mannitol YES NO YESYES YES YES YES YES NO D-Melibiose NO NO NO NO YES NO NO YES NO SucroseYES YES YES YES YES NO YES YES YES 2-Deoxy NO NO NO NO YES NO NO YES NOadenosine D-Cellobiose YES YES YES NO YES YES NO YES YES D-Malic acid NONO NO NO YES NO YES YES NO Phenylethyl- NO NO NO NO NO NO NO NO NO amineDulcitol NO NO YES YES YES YES NO YES NO L-Glutamic NO NO YES NO NO NOYES YES YES acid Thymidine NO NO NO NO NO NO NO NO NO Uridine NO NO NONO YES NO YES YES YES Adenosine NO YES NO NO NO NO YES NO YES Inosine NONO NO YES YES NO YES YES YES L-Malic acid NO NO YES NO YES YES YES YESYES 2-Amino- NO NO NO NO YES NO YES YES YES ethanol Strain/ SubstrateSYM00629 SYM00066 SYM00663 SYM00696 SYM00741A SYM00741B SYM00854SYM00880 D-Serine NO NO NO NO NO NO NO NO D-Glucose-6- NO NO NO NO NO NONO NO Phosphate L-Asparagine YES NO YES YES YES YES YES YES L-glutamineYES NO YES YES YES YES YES NO Glycyl-L- NO NO NO NO NO NO NO NO Asparticacid Glycyl-L- NO YES NO NO NO YES NO NO Glutamic acid Glycyl-L- NO NONO NO NO YES NO NO Proline L-Arabinose NO NO NO YES NO YES YES NOD-Sorbitol YES NO NO NO YES YES NO NO D-Galactonic NO NO NO NO NO YES NONO acid-?-lactone D-Aspartic acid NO NO YES NO NO NO YES NO m-Tartaricacid NO NO NO NO NO NO NO NO Citric acid YES NO YES NO YES YES YES NOTricarballylic NO NO NO NO NO NO NO NO acid p-Hydroxy NO YES NO NO NOYES NO NO Phenyl acetic acid N-Acetyl-D- YES NO YES NO NO YES YES NOGlucosamine Glycerol YES YES YES YES YES YES NO NO D-L-Malic acid YES NOYES NO NO YES YES YES D-Glucosaminic NO YES NO NO NO YES NO NO acidD-Glucose-1- NO YES NO NO NO NO NO NO Phosphate m-Inositol YES NO NO NONO YES NO NO L-Serine NO NO YES NO YES YES YES NO m-Hydroxy NO YES NO NONO NO NO NO Phenyl Acetic acid D-Saccharic NO NO NO YES NO YES YES NOacid L-Fucose NO NO NO NO NO NO NO NO D-Ribose YES NO NO NO NO YES NO NO1,2-Propanediol NO YES NO NO NO NO NO NO D-Fructose-6- NO NO NO NO NO NONO NO Phosphate D-Threonine NO NO NO NO NO NO NO NO L-Threonine NO NO NONO NO NO NO NO Tyramine YES NO NO NO NO NO NO NO Succinic acid YES YESNO NO NO YES YES NO D-Glucuronic YES NO YES NO YES YES NO NO acid Tween20 YES NO NO NO NO YES YES NO Tween 40 YES NO YES NO NO YES YES NO Tween80 YES YES YES NO NO YES YES NO Fumaric acid YES NO NO NO YES YES YES NOL-Alanine NO YES YES YES YES YES YES NO D-Psicose NO YES NO NO NO NO NONO D-Galactose NO NO NO YES NO YES YES NO D-Gluconic YES NO NO NO YESYES YES NO acid L-Rhamnose NO NO NO NO NO NO YES NO a-Keto-Glutaric YESNO YES NO YES YES YES NO acid a-Hydroxy NO NO NO NO NO YES NO NOGlutaric acid-?-lactone Bromo succinic NO NO NO NO NO YES YES NO acidL-Alanyl- YES NO YES NO NO YES YES NO Glycine L-Lyxose NO NO NO NO NO NOYES NO L-Aspartic acid YES NO YES NO NO YES YES NO D-L-a-Glycerol YES NOYES NO NO YES NO NO phosphate D-Fructose YES NO YES YES NO YES YES NOa-Keto-Butyric NO NO NO NO NO NO NO NO acid a-Hydroxy YES NO NO NO NO NONO NO Butyric acid Propionic acid NO NO YES NO NO YES NO NO AcetoaceticNO NO NO NO NO NO NO NO acid Glucuronamide NO NO NO NO NO NO NO NOL-Proline YES NO YES YES YES YES YES NO D-Xylose YES NO NO YES NO YESYES NO Acetic acid NO NO NO NO NO YES NO NO a-Methyl-D- NO NO NO NO NONO NO NO Galactoside β-Methyl-D- NO YES NO YES NO NO YES YES glucosideMucic acid YES NO YES NO YES YES YES NO N-acetyl-β-D- NO NO NO NO NO NONO NO Mannosamine Pyruvic acid NO NO YES NO NO YES NO NO D-Alanine YESNO NO NO NO YES YES NO L-Lactic acid NO NO YES YES NO YES NO NOa-D-Glucose YES YES YES YES YES YES YES NO a-D-Lactose NO NO YES YES NONO YES NO Adonitol YES NO YES NO NO YES YES NO Glycolic acid NO NO NO NONO NO NO NO Mono Methyl NO NO NO YES NO NO YES NO SuccinateL-Galactonic- YES NO NO YES NO YES YES NO acid-?-lactone D-Trehalose YESNO NO YES YES YES YES NO Formic acid NO NO NO NO NO NO NO NO Maltose NOYES YES YES YES NO YES YES Lactulose NO NO YES YES NO NO YES NOMaltotriose NO YES YES YES NO NO YES YES Glyoxylic acid NO NO NO NO NONO NO NO Methyl YES NO YES NO NO YES NO NO Pyruvate D-Galacturonic YESYES NO YES NO YES YES NO acid D-Mannose NO NO YES YES NO YES YES NOD-Mannitol YES YES NO NO NO YES YES NO D-Melibiose NO YES NO YES NO NOYES NO Sucrose YES NO YES YES YES YES YES YES 2-Deoxy NO NO NO NO NO NONO NO adenosine D-Cellobiose NO YES YES YES YES NO YES YES D-Malic acidYES NO NO NO NO NO YES NO Phenylethyl- NO NO NO NO NO NO NO NO amineDulcitol NO YES NO YES NO NO YES NO L-Glutamic YES NO YES YES NO YES YESNO acid Thymidine NO NO NO NO NO NO NO NO Uridine YES NO NO NO NO YESYES NO Adenosine YES NO NO NO NO YES NO NO Inosine YES NO YES YES NO YESNO NO L-Malic acid NO NO YES YES YES YES YES NO 2-Amino- YES NO NO NO NOYES NO NO ethanol

TABLE S Substrate utilization as determined by BIOLOG PM2A MicroPlatesby fungal endophytes belonging to core OTUs. Strain/Substrate SYM00120SYM00122 SYM00123 SYM00124 SYM00129 SYM01300 SYM01310 SYM01311N-acetyl-D- NO NO YES NO NO YES NO NO Galactosamine Gentiobiose NO NOYES YES YES NO NO YES D-Raffinose NO NO YES YES YES NO NO YES Capricacid NO NO NO NO NO YES NO NO D-lactic acid NO YES YES NO NO NO NO NOmethyl ester Acetamide NO NO YES NO NO NO NO NO L-Ornithine NO YES YESYES YES YES YES YES Chondrointin NO NO YES NO NO NO NO NO sulfate CN-acetyl- NO YES YES NO NO YES NO NO neuraminic acid L-glucose NO YES NONO NO NO NO NO Salicin YES NO NO YES NO NO NO YES Caproic acid NO NO NONO NO YES NO NO Malonic acid NO NO YES YES NO YES NO NO L-Alaninamide NONO YES NO NO YES NO NO L-Phenylalanine YES NO NO NO NO YES NO YESa-Cyclodextrin YES YES YES YES YES YES YES YES β-D-allose NO NO YES NONO NO NO NO Lactitol NO NO NO NO NO NO NO NO Sedoheptulosan YES YES NOYES NO NO NO NO Citraconic acid NO YES YES NO NO NO NO NO Melibionicacid NO NO NO NO NO NO NO NO N-Acetyl-L- NO NO NO NO NO YES YES NOGlutamic acid L-Pyroglutamic acid NO NO YES NO NO YES YES YESβ-Cyclodextrin NO YES YES NO NO NO NO NO Amygdalin NO NO NO YES NO NO NOYES D-Melezitose NO YES YES NO YES NO NO YES L-Sorbose NO NO YES NO YESNO NO NO Citramalic acid YES NO NO NO NO NO NO NO Oxalic acid NO NO YESYES NO NO NO NO L-Arginine NO NO NO YES NO YES YES YES L-Valine NO YESYES NO NO YES YES YES γ-Cyclodextrin NO NO YES YES NO NO NO NOD-arabinose NO NO NO YES NO NO NO NO Maltitol NO NO YES YES YES NO NOYES Stachyose NO NO NO YES NO NO NO YES D-Glucosamine NO NO NO NO NO YESNO NO Oxalomalic acid NO NO YES YES NO NO NO NO Glycine NO NO NO YES NONO NO NO D,L-Carnitine NO YES NO NO NO YES NO NO Dextrin NO NO YES NOYES NO NO YES D-arabitol NO YES NO YES NO NO NO YES a-Methyl-D- NO NO NONO NO NO NO NO Glucoside D-Tagatose NO NO NO YES NO NO NO NO 2-HydroxyNO YES NO NO NO NO NO NO benzoic acid Quinic acid NO NO NO NO NO YES NOYES L-Histidine NO NO NO NO YES YES YES YES Sec-Butylamine NO NO NO NONO NO NO NO Gelatin YES YES YES YES NO YES YES YES L-arabitol NO YES YESNO NO NO NO NO β-Methyl-D- NO NO YES NO NO NO NO YES GalactosideTuranose NO YES YES YES YES NO YES YES 4-Hydroxy NO NO YES NO NO NO NONO benzoic acid D-Ribono-1,4- NO YES YES NO NO NO NO NO LactoneL-Homoserine NO NO NO NO NO NO NO NO D,L-Octopamine NO NO YES NO NO YESYES YES Glycogen YES YES YES YES NO YES NO YES Arbutin NO NO YES YES NONO NO YES 3-Methyl Glucose YES NO NO NO NO NO NO NO Xylitol NO NO YES NONO NO NO NO β-Hydroxy butyric NO NO YES NO NO YES NO YES acid Sebacicacid YES YES YES NO NO YES NO NO Hydroxy-L-Proline NO NO NO YES NO YESYES YES Putrescine NO YES NO YES YES YES YES YES Inulin NO YES YES NO NONO NO NO 2-Deoxy-D-Ribose NO NO NO NO NO NO NO NO β-Methyl-D- YES YES NONO NO NO NO NO Glucuronic acid N-Acetyl-D- NO YES YES NO NO NO NO NOglucosaminitol γ-Hydroxy butyric NO YES YES NO NO NO NO NO acid Sorbicacid NO NO YES NO NO NO NO NO L-Isoleucine NO NO NO YES YES YES YES YESDihydroxy acetone NO NO YES NO NO NO NO NO Laminarin NO NO NO NO NO NONO NO i-Elythritol NO NO YES NO NO NO YES NO a-Methyl-D- NO NO YES NO NONO NO NO Mannoside γ-amino butyric acid NO YES NO NO YES YES YES YESa-Keto-valeric acid NO NO YES NO NO NO NO NO Succinamic acid NO NO YESNO NO YES NO NO L-Leucine NO NO NO YES NO YES YES YES 2,3-Butanediol YESNO YES NO NO NO NO NO Mannan NO NO YES NO NO NO NO NO D-Fucose NO NO NONO NO NO NO NO β-Methly-D-Xyloside NO YES NO NO NO NO NO NO d-aminovaleric acid NO YES YES NO NO NO NO YES Itaconic acid NO NO YES NO NO NONO NO D-Tartaric acid NO YES NO NO NO NO NO NO L-Lysine NO NO YES NO NONO NO YES 2,3-Butanone NO NO YES NO NO NO NO NO Pectin NO YES NO YES NONO NO YES 3-0-β-D- NO NO YES NO NO NO YES NO Galactopyranosyl-D-arabinose Palatinose NO NO YES YES YES NO NO YES Butyric acid NO YESNO NO NO NO YES NO 5-Keto-D-Gluconic NO NO NO NO NO NO NO YES acidL-Tartaric acid NO NO YES NO NO NO NO YES L-Methionine NO YES NO NO NONO NO NO 3-Hydroxy 2- NO NO NO NO NO NO NO NO Butanone Strain/SubstrateSYM01314 SYM01315 SYM01324 SYM01325 SYM01326 SYM01327 SYM01333N-acetyl-D- YES YES NO NO NO YES NO Galactosamine Gentiobiose NO YES YESYES NO NO NO D-Raffinose NO NO NO YES YES NO NO Capric acid YES NO NO NOYES YES YES D-lactic acid NO NO NO NO NO NO NO methyl ester Acetamide NONO NO NO NO NO NO L-Ornithine YES YES NO YES YES YES YES Chondrointin NOYES NO NO NO NO NO sulfate C N-acetyl- YES NO NO NO NO YES NO neuraminicacid L-glucose NO NO NO NO NO NO NO Salicin NO NO NO YES YES NO NOCaproic acid NO NO NO NO YES NO NO Malonic acid NO NO NO NO NO NO NOL-Alaninamide YES NO NO YES YES YES YES L-Phenylalanine YES NO NO NO NOYES NO a-Cyclodextrin YES YES YES YES YES YES YES β-D-allose NO YES NONO NO NO NO Lactitol NO YES YES NO NO NO NO Sedoheptulosan NO NO NO NONO NO NO Citraconic acid NO YES NO NO NO NO NO Melibionic acid YES YESNO NO NO NO NO N-Acetyl-L- YES NO NO NO YES YES YES Glutamic acidL-Pyroglutamic acid YES YES NO YES YES YES YES β-Cyclodextrin NO NO NONO NO NO NO Amygdalin NO NO NO YES NO NO NO D-Melezitose NO NO YES YESNO NO NO L-Sorbose NO NO NO NO NO NO NO Citramalic acid NO NO NO NO NOYES NO Oxalic acid NO NO NO NO NO NO NO L-Arginine YES YES NO YES YESYES YES L-Valine YES NO NO YES YES YES YES γ-Cyclodextrin NO YES NO YESNO NO YES D-arabinose NO YES NO NO NO NO NO Maltitol NO NO YES NO NO NONO Stachyose NO NO YES YES NO NO NO D-Glucosamine YES NO NO NO NO YES NOOxalomalic acid NO YES NO NO NO NO NO Glycine NO NO NO NO NO YES NOD,L-Carnitine YES NO NO NO YES YES NO Dextrin NO YES NO YES NO NO NOD-arabitol NO YES YES YES NO NO YES a-Methyl-D- NO NO YES NO NO NO NOGlucoside D-Tagatose NO NO NO NO NO NO NO 2-Hydroxy benzoic YES YES NONO YES NO NO acid Quinic acid YES NO YES YES NO NO NO L-Histidine YESYES YES NO YES YES YES Sec-Butylamine NO NO NO NO NO NO NO Gelatin YESYES YES YES YES YES YES L-arabitol NO YES NO NO NO NO NO β-Methyl-D- NONO NO NO NO NO NO Galactoside Turanose NO NO NO NO NO NO NO 4-Hydroxy NOYES NO NO NO NO NO benzoic acid D-Ribono-1,4- NO YES NO NO YES NO NOLactone L-Homoserine NO NO NO NO NO NO NO D,L-Octopamine YES NO NO NOYES YES YES Glycogen NO YES YES YES YES NO NO Arbutin NO YES YES YES NONO NO 3-Methyl Glucose NO NO NO NO NO NO NO Xylitol NO YES NO NO NO NONO β-Hydroxy butyric NO YES YES YES NO YES YES acid Sebacic acid NO YESNO NO NO NO NO Hydroxy-L-Proline YES YES NO YES YES YES YES PutrescineNO YES NO YES NO NO NO Inulin NO YES NO NO YES NO NO 2-Deoxy-D-Ribose NONO NO NO NO NO NO β-Methyl-D- NO YES NO NO NO NO NO Glucuronic acidN-Acetyl-D- NO NO NO NO NO NO NO glucosaminitol γ-Hydroxy butyric NO YESNO NO NO NO NO acid Sorbic acid NO NO NO NO NO NO NO L-Isoleucine YES NONO YES YES YES YES Dihydroxy acetone NO NO NO NO NO NO NO Laminarin NONO NO YES NO NO NO i-Elythritol NO YES NO NO NO NO YES a-Methyl-D- NOYES NO NO NO NO NO Mannoside γ-amino butyric acid YES YES YES YES YESYES YES a-Keto-valeric acid NO YES NO NO NO NO NO Succinamic acid YESYES NO YES YES YES NO L-Leucine YES YES NO NO YES YES YES 2,3-ButanediolNO NO NO NO NO NO NO Mannan NO NO NO NO NO NO NO D-Fucose NO NO NO NO NONO NO β-Methly-D-Xyloside NO YES NO NO NO NO NO d-amino valeric acid NOYES NO NO NO NO NO Itaconic acid NO YES NO NO NO NO NO D-Tartaric acidNO YES NO NO NO NO NO L-Lysine NO YES NO YES NO NO NO 2,3-Butanone NOYES NO NO NO NO NO Pectin NO YES NO NO NO NO NO 3-0-β-D- NO YES YES NONO NO YES Galactopyranosyl- D-arabinose Palatinose NO YES YES YES NO NONO Butyric acid NO NO NO NO NO NO NO 5-Keto-D-Gluconic NO YES NO YES NONO NO acid L-Tartaric acid NO NO NO NO NO NO NO L-Methionine NO NO NO NONO NO NO 3-Hydroxy 2- NO YES NO NO NO NO NO Butanone

TABLE T Substrate utilization as determined by BIOLOG PM2A MicroPlatesby fungal endophytes belonging to core OTUs. Strain/Substrate SYM00135SYM00136 SYM00151 SYM00154 SYM15811 SYM15820 SYM15825 SYM15828 SYM15831N-acetyl-D- NO NO NO NO NO NO NO NO NO Galactosamine Gentiobiose NO YESYES NO NO NO YES NO NO D-Raffinose YES YES YES YES YES NO YES NO YESCapric acid NO NO NO NO YES NO NO NO NO D-lactic acid NO NO NO NO YES NONO NO NO methyl ester Acetamide NO NO NO NO NO NO NO NO NO L-OrnithineYES NO YES NO NO YES YES YES YES Chondrointin NO NO NO NO NO NO NO NO NOsulfate C N-acetyl- NO NO NO NO NO NO NO NO NO neuraminic acid L-glucoseNO NO NO NO NO NO NO NO NO Salicin NO NO YES NO YES NO YES NO YESCaproic acid NO NO NO NO YES NO NO NO NO Malonic acid NO NO YES NO NO NOYES NO NO L-Alaninamide NO NO YES NO YES NO YES NO NO L-Phenylalanine NONO YES NO NO NO YES NO NO a-Cyclodextrin YES YES YES YES YES NO NO YESYES β-D-allose NO NO NO NO NO NO NO NO NO Lactitol NO NO NO NO YES NO NONO NO Sedoheptulosan NO NO NO NO NO NO NO NO NO Citraconic acid NO NO NONO NO NO NO NO NO Melibionic acid NO NO NO NO NO NO NO NO NO N-Acetyl-L-NO NO NO NO NO YES NO YES NO Glutamic acid L-Pyroglutamic NO YES YES NOYES YES YES YES YES acid β-Cyclodextrin NO NO NO NO NO NO NO NO NOAmygdalin NO NO YES NO NO NO YES NO NO D-Melezitose YES YES YES NO YESNO YES NO YES L-Sorbose NO YES YES NO NO NO NO NO NO Citramalic acid NONO NO NO NO NO NO NO NO Oxalic acid NO YES NO NO NO NO NO NO NOL-Arginine NO NO YES NO NO YES YES YES YES L-Valine NO NO NO NO NO YESYES YES NO γ-Cyclodextrin NO YES NO NO NO NO YES NO NO D-arabinose NO NONO NO NO NO NO NO NO Maltitol NO YES YES NO NO NO YES NO NO StachyoseYES YES YES NO NO NO YES NO YES D-Glucosamine NO NO NO NO NO NO NO NOYES Oxalomalic NO NO NO NO NO NO NO NO NO acid Glycine NO NO NO NO YESNO YES NO NO D,L-Carnitine NO NO NO NO NO NO NO NO YES Dextrin YES NOYES NO YES NO YES NO YES D-arabitol YES NO YES NO NO NO YES NO NOa-Methyl-D- NO NO NO NO NO NO NO NO NO Glucoside D-Tagatose NO NO NO NONO NO NO NO NO 2-Hydroxy NO NO NO NO NO NO NO NO NO benzoic acid Quinicacid NO NO YES NO YES NO YES NO NO L-Histidine NO YES NO NO YES YES YESYES NO Sec-Butylamine NO NO NO NO NO NO NO NO NO Gelatin NO NO YES NO NOYES YES YES NO L-arabitol NO NO NO NO NO NO NO NO NO β-Methyl-D- NO YESNO NO NO NO NO NO NO Galactoside Turanose YES YES YES YES NO NO YES NOYES 4-Hydroxy NO NO NO NO NO NO NO NO NO benzoic acid D-Ribono- NO NO NONO YES NO NO NO NO 1,4-Lactone L-Homoserine NO NO NO NO NO NO NO NO NOD,L- NO NO NO NO YES YES NO YES NO Octopamine Glycogen NO YES YES NO NONO YES NO YES Arbutin NO YES YES NO NO NO YES NO NO 3-Methyl NO NO NO NONO NO NO NO NO Glucose Xylitol NO NO NO NO YES NO NO NO NO β-Hydroxy NONO YES NO NO NO NO NO NO butyric acid Sebacic acid NO NO NO NO NO NO YESNO NO Hydroxy-L- NO NO YES NO YES YES YES YES YES Proline Putrescine YESYES YES NO NO NO YES YES NO Inulin NO NO NO NO NO NO NO NO NO 2-Deoxy-D-NO NO NO NO NO NO NO NO NO Ribose β-Methyl-D- NO NO NO NO NO NO NO NO NOGlucuronic acid N-Acetyl-D- NO NO NO NO NO NO NO NO NO glucosaminitolγ-Hydroxy NO NO NO NO YES NO NO NO NO butyric acid Sorbic acid NO NO NONO NO NO NO NO NO L-Isoleucine NO NO YES NO NO YES YES YES YES DihydroxyNO NO NO NO NO NO NO NO NO acetone Laminarin NO NO YES NO NO NO NO NO NOi-Erythritol NO NO NO NO NO NO NO NO NO a-Methyl-D- NO NO NO NO NO NO NONO NO Mannoside γ-amino NO YES YES NO YES NO YES NO YES butyric acida-Keto- NO NO NO NO NO NO NO NO NO valeric acid Succinamic acid NO NO NONO NO NO YES NO NO L-Leucine NO NO YES YES NO NO YES NO NO2,3-Butanediol NO NO NO NO NO NO NO NO NO Mannan NO NO NO NO NO NO NO NONO D-Fucose NO NO NO NO NO NO NO NO NO β-Methyl- NO NO NO NO NO NO NO NONO D-Xyloside d-amino NO NO NO NO NO NO NO NO NO valeric acid Itaconicacid NO NO NO NO YES NO NO NO NO D-Tartaric acid NO NO NO NO NO NO NO NONO L-Lysine NO NO YES NO NO NO YES NO YES 2,3-Butanone NO NO NO NO NO NONO NO NO Pectin NO NO YES NO NO NO YES YES YES 3-0-β-D- NO NO NO NO NONO YES NO NO Galacto- pyranosyl- D-arabinose Palatinose YES YES YES NOYES NO YES NO YES Butyric acid NO NO NO NO YES NO YES YES NO 5-Keto-D-NO NO NO NO NO NO NO NO NO Gluconic acid L-Tartaric acid NO NO YES NOYES NO YES NO NO L-Methionine NO NO NO NO NO NO NO NO NO 3-Hydroxy NO NONO NO NO NO NO NO NO 2-Butanone Strain/Substrate SYM15837 SYM15839SYM15847 SYM15872 SYM15890 SYM15901 SYM15920 SYM15926 N-acetyl-D- NO NONO NO NO NO NO NO Galactosamine Gentiobiose NO YES YES YES NO YES YES NOD-Raffinose YES YES YES YES NO YES YES NO Capric acid NO NO NO NO NO NONO NO D-lactic acid NO NO NO NO NO NO NO NO methyl ester Acetamide NO NONO NO NO NO NO NO L-Ornithine YES YES YES YES YES YES YES YESChondrointin NO NO NO YES NO NO NO NO sulfate C N-acetyl- NO NO NO NO NONO NO NO neuraminic acid L-glucose NO NO NO NO NO NO NO NO Salicin NOYES YES YES NO YES YES NO Caproic acid NO NO NO NO NO NO NO NO Malonicacid YES NO NO YES NO NO NO NO L-Alaninamide NO NO YES YES NO NO NO NOL-Phenylalanine NO YES YES YES NO YES YES NO a-Cyclodextrin YES YES YESYES YES YES YES YES β-D-allose NO NO NO NO NO NO NO NO Lactitol NO NO NONO NO NO NO NO Sedoheptulosan NO NO YES YES NO NO NO NO Citraconic acidNO NO NO NO NO NO NO NO Melibionic acid NO NO NO NO NO NO NO NON-Acetyl-L- YES NO NO NO NO NO NO YES Glutamic acid L-Pyroglutamic YESYES YES YES YES YES YES NO acid β-Cyclodextrin NO NO NO NO NO NO NO NOAmygdalin YES YES YES YES NO YES YES NO D-Melezitose YES YES YES YES NOYES YES NO L-Sorbose YES YES NO NO NO YES NO NO Citramalic acid NO NO NONO NO NO NO NO Oxalic acid NO NO NO YES NO NO NO YES L-Arginine YES YESYES YES NO YES YES NO L-Valine YES YES NO YES NO YES YES YESγ-Cyclodextrin NO YES NO YES NO YES YES NO D-arabinose NO NO NO YES NONO NO NO Maltitol NO NO NO YES NO YES YES YES Stachyose YES YES YES YESNO YES YES NO D-Glucosamine YES YES NO NO NO NO NO NO Oxalomalic NO NONO NO NO NO NO NO acid Glycine NO NO YES YES NO YES NO NO D,L-CarnitineYES NO NO NO NO NO NO NO Dextrin YES YES NO YES NO YES YES YESD-arabitol NO NO NO YES NO YES YES NO a-Methyl-D- NO YES NO YES NO NOYES NO Glucoside D-Tagatose NO NO NO NO NO NO NO NO 2-Hydroxy NO NO NONO NO NO NO NO benzoic acid Quinic acid NO YES NO YES NO NO YES NOL-Histidine NO YES NO YES NO YES YES YES Sec-Butylamine NO NO NO NO NOYES NO NO Gelatin YES YES YES YES YES YES YES YES L-arabitol NO NO NOYES NO NO NO NO β-Methyl-D- YES NO NO YES NO NO NO NO GalactosideTuranose YES YES YES YES NO YES YES NO 4-Hydroxy NO NO NO YES NO NO NONO benzoic acid D-Ribono- NO NO NO NO NO NO NO NO 1,4-LactoneL-Homoserine NO NO NO NO NO NO NO NO D,L- YES NO NO NO YES NO NO NOOctopamine Glycogen YES YES YES YES NO YES YES NO Arbutin YES YES YESYES NO YES YES NO 3-Methyl NO NO NO NO NO NO NO NO Glucose Xylitol NO NONO YES NO NO NO NO β-Hydroxy NO NO NO NO YES YES YES NO butyric acidSebacic acid YES NO NO YES NO NO NO NO Hydroxy-L- YES YES YES YES YESYES YES YES Proline Putrescine NO YES YES YES NO YES YES NO Inulin YESNO NO NO YES NO NO NO 2-Deoxy-D- NO NO NO NO NO NO NO NO Riboseβ-Methyl-D- NO NO NO YES NO NO NO YES Glucuronic acid N-Acetyl-D- NO NONO NO NO NO NO NO glucosaminitol γ-Hydroxy NO NO NO NO NO NO NO NObutyric acid Sorbic acid NO NO NO NO NO NO NO NO L-Isoleucine YES YESYES YES NO YES YES NO Dihydroxy NO NO NO NO NO NO NO NO acetoneLaminarin NO YES NO NO YES NO YES NO i-Erythritol YES NO NO NO NO NO NONO a-Methyl-D- NO NO NO NO NO NO NO NO Mannoside γ-amino YES YES YES YESNO YES YES YES butyric acid a-Keto- YES NO NO YES YES NO NO NO valericacid Succinamic acid YES NO YES YES NO YES NO NO L-Leucine YES YES YESYES NO YES YES NO 2,3-Butanediol NO NO NO YES NO NO NO NO Mannan NO NONO NO NO NO NO NO D-Fucose NO NO NO NO NO NO NO NO β-Methyl- NO NO NO NONO NO NO NO D-Xyloside d-amino NO NO YES YES NO YES NO YES valeric acidItaconic acid YES NO NO NO NO NO NO YES D-Tartaric acid NO NO NO NO NONO NO NO L-Lysine YES NO YES YES NO YES NO NO 2,3-Butanone NO NO NO NONO NO NO NO Pectin YES YES NO YES NO YES YES YES 3-0-β-D- NO NO NO YESNO NO NO NO Galacto- pyranosyl- D-arabinose Palatinose YES YES YES YESYES YES YES NO Butyric acid YES NO NO YES NO YES YES NO 5-Keto-D- NO NONO NO NO YES NO NO Gluconic acid L-Tartaric acid NO NO NO YES NO YES YESNO L-Methionine NO NO NO NO NO NO NO NO 3-Hydroxy NO NO NO NO NO NO NONO 2-Butanone

TABLE U Substrate utilization as determined by BIOLOG PM2A MicroPlatesby fungal endophytes belonging to core OTUs. SYM- SYM- SYM- SYM- SYM-SYM- SYM- SYM- SYM- Strain/Substrate 159298 15932 00160 00034 00566B00577 00590 00603 00061A N-acetyl-D-Galactosamine NO NO NO NO NO NO NONO NO Gentiobiose YES YES YES YES NO YES YES NO YES D-Raffinose YES YESYES NO NO YES NO NO YES Capric acid NO NO NO NO NO NO NO YES NO D-lacticacid methyl ester NO NO NO NO NO NO NO NO NO Acetamide NO NO NO NO NO NONO NO NO L-Ornithine YES YES NO YES NO YES YES YES YES Chondrointinsulfate C NO YES NO NO NO NO NO NO NO N-acetyl-neuraminic acid NO NO NONO NO NO NO NO NO L-glucose NO NO NO NO NO NO NO NO NO Salicin YES YESYES YES NO YES YES NO YES Caproic acid NO NO NO NO NO NO NO NO NOMalonic acid NO NO NO NO YES NO NO NO YES L-Alaninamide NO NO NO YES NOYES NO YES YES L-Phenylalanine NO NO NO NO NO YES NO YES NOa-Cyclodextrin YES YES YES YES YES NO NO YES YES β-D-allose YES NO NO NONO NO NO NO NO Lactitol NO NO NO NO NO NO NO NO YES Sedoheptulosan NO NONO NO NO NO NO NO NO Citraconic acid NO NO NO NO NO NO NO NO NOMelibionic acid NO NO NO NO NO YES NO NO YES N-Acetyl-L-Glutamic acid NONO NO NO NO NO NO YES NO L-Pyroglutamic acid YES NO NO YES YES YES NOYES YES β-Cyclodextrin NO YES YES NO NO NO NO NO NO Amygdalin NO YES NOYES NO YES NO NO NO D-Melezitose YES YES YES YES NO YES NO NO YESL-Sorbose NO NO NO NO NO YES NO NO NO Citramalic acid NO NO NO NO NO NONO NO NO Oxalic acid NO YES NO NO NO NO NO NO NO L-Arginine YES YES NOYES NO YES NO YES YES L-Valine NO NO NO YES NO YES NO YES NOγ-Cyclodextrin YES YES YES NO NO YES NO NO YES D-arabinose NO NO NO NONO NO NO NO NO Maltitol YES YES YES NO NO YES NO NO YES Stachyose YESYES YES NO NO YES NO NO YES D-Glucosamine NO NO NO YES NO YES NO YES NOOxalomalic acid NO NO NO NO NO NO NO NO NO Glycine NO NO NO NO NO NO NONO NO D,L-Carnitine NO NO NO NO NO NO NO YES NO Dextrin YES YES YES YESNO YES NO NO YES D-arabitol YES NO NO YES NO YES NO NO YESa-Methyl-D-Glucoside YES NO YES NO NO NO NO NO NO D-Tagatose NO NO NO NONO NO NO NO NO 2-Hydroxy benzoic acid NO NO NO NO NO NO NO NO NO Quinicacid NO YES NO YES NO NO NO YES NO L-Histidine NO NO NO NO YES YES NOYES YES Sec-Butylamine NO NO NO NO NO NO NO NO NO Gelatin YES YES NO YESNO YES YES NO YES L-arabitol NO YES NO NO NO NO NO NO YESβ-Methyl-D-Galactoside NO YES NO YES NO NO NO NO YES Turanose YES YESYES YES NO YES NO NO YES 4-Hydroxy benzoic acid NO NO NO NO NO NO NO NOYES D-Ribono-1,4-Lactone NO NO NO NO NO NO NO NO NO L-Homoserine NO NONO NO NO NO NO NO YES D,L-Octopamine NO NO NO NO NO YES NO YES YESGlycogen YES YES YES YES NO YES YES NO YES Arbutin YES YES YES YES NOYES YES NO YES 3-Methyl Glucose NO NO NO NO NO NO NO NO NO Xylitol NO NOYES NO YES NO NO NO NO β-Hydroxy butyric acid YES NO NO NO YES YES NO NONO Sebacic acid NO NO NO NO NO NO NO NO YES Hydroxy-L-Proline NO NO NONO YES YES YES YES YES Putrescine YES NO NO YES NO YES NO YES YES InulinYES NO NO NO NO NO YES NO NO 2-Deoxy-D-Ribose NO NO NO NO NO NO NO NO NOβ-Methyl-D-Glucuronic acid NO YES NO NO NO NO NO NO YESN-Acetyl-D-glucosaminitol NO NO NO NO NO NO NO NO NO γ-Hydroxy butyricacid NO NO NO NO NO NO NO NO YES Sorbic acid NO NO NO NO YES NO NO NOYES L-Isoleucine NO YES NO YES NO YES NO YES NO Dihydroxy acetone NO NONO NO NO NO NO NO NO Laminarin NO NO NO YES NO NO NO NO YES i-ErythritolYES NO NO YES NO NO YES NO NO a-Methyl-D-Mannoside NO NO NO NO NO NO NONO NO γ-amino butyric acid YES NO NO YES NO YES YES YES YESa-Keto-valeric acid NO YES NO NO YES NO NO NO YES Succinamic acid NO NONO YES NO NO NO NO YES L-Leucine NO NO NO YES NO YES NO YES NO2,3-Butanediol NO NO NO NO NO NO NO NO YES Mannan NO NO NO NO NO NO NONO NO D-Fucose NO YES NO NO NO NO NO NO NO β-Methyl-D-Xyloside NO NO NONO NO NO NO NO NO d-amino valeric acid NO NO NO NO NO YES NO NO YESItaconic acid NO NO NO NO NO NO NO NO NO D-Tartaric acid NO NO NO NO NONO NO NO NO L-Lysine NO NO NO YES YES NO NO NO YES 2,3-Butanone NO NO NONO NO NO NO NO NO Pectin YES YES YES YES NO YES NO NO YES3-0-β-D-Galactopyranosyl- NO NO NO NO NO YES NO NO NO D-arabinosePalatinose YES YES YES YES NO YES YES NO NO Butyric acid NO NO NO NO NONO NO NO YES 5-Keto-D-Gluconic acid NO NO NO NO NO NO NO NO NOL-Tartaric acid NO YES NO NO NO YES NO NO YES L-Methionine NO NO YES NONO NO NO NO NO 3-Hydroxy 2-Butanone NO NO NO NO NO NO NO NO NO SYM- SYM-SYM- SYM- SYM- SYM- SYM- SYM- SYM- Strain/Substrate 00622 00629 0006600663 00696 00741A 00741B 00854 00880 N-acetyl-D-Galactosamine NO NO NONO NO NO NO NO YES Gentiobiose NO NO NO NO YES YES NO NO NO D-RaffinoseNO NO YES NO YES YES NO YES NO Capric acid NO NO NO NO NO NO NO NO NOD-lactic acid methyl ester NO NO NO NO NO NO NO NO NO Acetamide NO NO NONO YES NO NO NO YES L-Ornithine YES YES NO YES YES YES YES NO NOChondrointin sulfate C NO NO NO NO YES YES NO NO NO N-acetyl-neuraminicacid NO NO NO NO NO NO NO NO YES L-glucose NO NO NO NO NO YES NO NO NOSalicin NO NO NO NO YES NO NO NO NO Caproic acid NO NO NO NO YES NO NONO NO Malonic acid NO NO NO NO NO NO NO NO NO L-Alaninamide NO NO NO NOYES NO YES NO YES L-Phenylalanine NO NO NO NO NO YES NO NO NOa-Cyclodextrin YES NO YES NO NO NO YES NO YES β-D-allose NO NO NO NO YESNO NO NO YES Lactitol NO NO NO NO YES YES NO NO YES Sedoheptulosan NO NONO NO NO YES NO NO YES Citraconic acid NO NO NO NO YES NO NO NO YESMelibionic acid NO NO NO NO NO YES NO NO NO N-Acetyl-L-Glutamic acid YESYES NO NO YES NO YES NO YES L-Pyroglutamic acid YES NO NO YES NO YES YESYES YES β-Cyclodextrin NO NO NO NO NO YES NO NO YES Amygdalin NO NO NONO NO YES NO YES YES D-Melezitose NO NO NO NO YES YES NO NO YESL-Sorbose NO NO NO NO NO YES NO NO NO Citramalic acid NO NO NO NO NO NONO NO YES Oxalic acid NO NO NO NO YES NO NO NO YES L-Arginine YES YES NOYES YES YES YES YES YES L-Valine YES YES NO NO YES YES YES NO YESγ-Cyclodextrin NO NO NO NO YES NO NO YES NO D-arabinose NO NO NO NO YESNO NO NO NO Maltitol NO NO NO NO YES YES NO YES YES Stachyose NO NO NONO YES YES NO YES YES D-Glucosamine YES NO NO NO NO NO NO NO NOOxalomalic acid NO NO NO NO NO NO NO NO NO Glycine NO NO NO NO YES YESNO NO YES D,L-Carnitine YES NO NO NO NO NO YES NO NO Dextrin NO NO NO NOYES YES NO YES YES D-arabitol NO YES NO NO YES YES NO YES NOa-Methyl-D-Glucoside NO NO NO NO NO YES NO NO NO D-Tagatose NO NO NO YESNO NO NO NO NO 2-Hydroxy benzoic acid NO NO NO NO YES YES NO NO NOQuinic acid NO NO NO NO YES NO NO NO YES L-Histidine YES NO NO NO YES NOYES NO NO Sec-Butylamine NO NO NO NO NO NO NO NO NO Gelatin NO NO NO NOYES YES YES YES NO L-arabitol NO NO NO NO YES NO NO NO YESβ-Methyl-D-Galactoside NO NO NO NO YES NO NO NO NO Turanose NO NO NO NOYES NO NO YES YES 4-Hydroxy benzoic acid NO NO NO NO YES NO NO NO YESD-Ribono-1,4-Lactone NO NO NO YES YES NO NO YES YES L-Homoserine NO NONO NO NO NO NO NO NO D,L-Octopamine YES YES NO NO NO YES YES YES NOGlycogen YES NO NO YES YES YES NO YES YES Arbutin NO NO NO NO YES YESYES YES YES 3-Methyl Glucose NO NO NO NO NO YES NO NO NO Xylitol NO NONO NO NO NO NO NO YES β-Hydroxy butyric acid NO NO NO NO YES YES NO NONO Sebacic acid YES NO NO NO NO NO NO NO NO Hydroxy-L-Proline YES YES NOYES NO YES YES YES YES Putrescine NO NO NO NO YES YES NO NO YES InulinYES YES NO NO YES YES YES NO YES 2-Deoxy-D-Ribose NO NO NO NO NO NO NONO NO β-Methyl-D-Glucuronic acid NO NO NO NO YES NO NO NO NON-Acetyl-D-glucosaminitol NO NO NO NO YES NO NO NO YES γ-Hydroxy butyricacid NO NO NO NO YES NO NO NO NO Sorbic acid NO NO NO NO NO NO NO NO NOL-Isoleucine YES YES NO NO YES YES YES NO YES Dihydroxy acetone NO NO NONO NO NO NO NO NO Laminarin NO NO NO NO NO NO NO NO NO i-Erythritol NOYES NO NO YES NO YES YES NO a-Methyl-D-Mannoside NO NO NO NO YES NO NONO NO γ-amino butyric acid YES YES NO NO YES YES YES YES YESa-Keto-valeric acid NO NO NO NO YES NO NO NO YES Succinamic acid NO NONO NO YES YES NO YES YES L-Leucine YES YES NO NO NO YES YES NO NO2,3-Butanediol NO NO NO NO YES NO NO NO YES Mannan NO NO NO NO YES NO NONO YES D-Fucose NO NO NO NO YES NO NO NO YES β-Methyl-D-Xyloside NO NONO NO NO NO NO NO NO d-amino valeric acid NO NO NO NO NO NO NO NO NOItaconic acid NO NO NO NO YES NO NO NO NO D-Tartaric acid NO NO NO NOYES NO NO NO NO L-Lysine NO NO NO NO YES YES NO NO YES 2,3-Butanone NONO NO NO NO NO NO NO NO Pectin NO NO NO NO YES YES NO YES YES3-0-β-D-Galactopyranosyl- NO NO NO NO YES YES YES NO YES D-arabinosePalatinose NO NO NO YES YES YES NO YES YES Butyric acid NO NO NO NO NONO NO YES NO 5-Keto-D-Gluconic acid NO NO NO NO YES NO NO NO NOL-Tartaric acid NO NO NO NO NO NO NO NO NO L-Methionine NO NO NO NO NONO NO NO NO 3-Hydroxy 2-Butanone NO NO NO YES NO NO NO NO NO

Characterization of Culturable Microbes: Substrate Use

Additional BIOLOG analyses were performed. For additional biologanalyses, microbes were cultivated in three biological replicates foreach strain. Each bacterium was initially streaked on Reasoner's 2A(R2A) agar, distinct CFUs selected and cultured in 6 mL R2A broth for 4days. Fungal strains were streaked on potato dextrose (PD) agar andindividual plugs containing spores and mycelial tissues were used toinitiate growth in 6 mL PD broth for 6 days. All strains were grown withagitation at room temperature. One mL liquid cultures of each samplewere harvested by centrifugation for 15 minutes at 4500 RPM andsubsequently washed at least four times with sterile distilled water toremove any traces of residual media. Additionally, fungal cultures werefirst sonicated to achieve homogeneity after the growth period. Microbeswere resuspended in 500 μL sterile distilled water and measurements ofabsorbance were taken using a SpectraMax M microplate reader (MolecularDevices, Sunnyvale, Calif.).

Sole carbon substrate assays were done using BIOLOG Phenotype MicroArray(PM) 1 and 2A MicroPlates (Hayward, Calif.). An aliquot of eachbacterial cell culture corresponding to a final absorbance of 0.2 wereinoculated into 20 mL sterile IF-0a GN/GP Base inoculating fluid (IF-0),0.24 mL 100× Dye B obtained from BIOLOG, and brought to a final volumeof 24 mL with sterile distilled water in 50 mL Falcon tubes. Negativecontrol PM1 and PM2A assays were done similarly for each dye minusbacterial cells to detect abiotic reactions. Fungal culture of eachstrain with a final absorbance of 0.2 (˜63% turbidity) was brought to afinal volume of 24 mL with the FF-IF medium (BIOLOG). Microbial cellsuspensions in tubes were gently shaken to achieve uniformity. Onehundred microliters of the microbial cell suspension was added per wellusing a multichannel pipettor to the 96-well BIOLOG PM1 and PM2AMicroPlates that each contained 95 carbon sources and one water-only(negative control) well. All steps were performed under sterileconditions using biosafety cabinets.

MicroPlates were sealed in paper surgical tape (Dynarex, Orangeburg,N.Y.) to minimize plate edge effects, and incubated stationary at 24° C.in an enclosed container for a minimum of 72 hours. Absorbance at 590 nmwas measured for all MicroPlates at least every 24 hours or at a definedinterval (72 hours post-assay) to determine carbon substrate utilizationfor each strain. Measurements were normalized relative to the negativecontrol (water only) well of each plate (Garland and Mills, 1991; Baruaet al., 2010; Siemens et al., 2012; Blumenstein et al., 2015). BacterialMicroPlates were also visually examined for the irreversible formationof violet color in wells indicating the reduction of the tetrazoliumredox dye to formazan that result from cell respiration (Garland andMills, 1991), and assessed against the negative control (no cells) PM1and PM2A MicroPlates to detect any abiotic color changes potentiallyintroduced by the medium and/or dyes (Borglin et al., 2012). Normalizedabsorbance values that were negative were considered as zero forsubsequent analysis (Garland and Mills, 1991; Blumenstein et al., 2015)and a threshold value of 0.1 and above was used to indicate the abilityof a particular microbial strain to use a given carbon substrate (Baruaet al., 2010; Blumenstein et al., 2015). Fungal PM tests were measuredas growth assays and visual observation of mycelial growth in each wellwas made.

TABLE V Substrate utilization as determined by BIOLOG PM1 MicroPlates bybacterial endophytes belonging to OTUs present in cereal seeds, fruitseeds, vegetable seeds, and oil seeds. SYM- SYM- SYM- SYM- SYM- SYM-SYM- SYM- SYM- SYM- SYM- SYM- SYM- SYM- SYM- SYM- SYM- Strain/Substrate00021b 00044 00057b 00074 00091 00092d 00212 00290 00619 00865 0087900879b 00906 00965 01004 01022 01158 1,2-Propanediol NO NO NO NO NO NONO NO NO NO NO NO NO NO YES NO NO 2-Aminoethanol NO NO NO NO NO NO NO NONO NO NO NO NO NO YES NO YES 2′- YES YES YES YES YES YES YES NO YES YESNO YES YES YES YES YES NO Deoxyadenosine a-D-Glucose YES YES YES YES YESYES YES NO YES YES YES YES YES YES YES YES YES a-D-Lactose YES YES YESYES YES YES YES NO NO YES YES YES YES YES YES YES NO a-Hydroxybutyric NONO NO NO YES NO NO YES NO NO NO YES YES YES NO NO YES acida-Hydroxyglutaric NO NO NO NO YES NO NO NO YES YES NO YES NO YES YES YESNO acid-g-Lactone a-Ketobutyric NO NO NO NO YES NO NO YES YES NO NO YESYES YES NO NO YES acid a-Ketoglutaric YES NO NO NO YES NO NO NO YES YESYES YES YES YES YES YES YES acid a-Methyl-D- YES YES YES YES YES NO YESNO NO YES YES YES YES YES YES YES NO Galactoside Acetic acid YES YES YESYES YES YES YES YES YES YES YES YES YES YES YES YES YES Acetoacetic acidNO NO NO NO NO NO NO NO NO NO NO NO NO NO NO NO NO Adenosine YES YES YESYES YES YES YES NO YES YES NO YES YES YES YES YES NO Adonitol YES YESYES YES YES NO YES NO YES YES NO YES NO YES YES NO YES Ala-Gly YES YESYES YES YES YES YES NO YES YES NO YES YES YES YES YES YES b-Methyl-D-YES YES YES YES YES YES YES YES YES YES YES YES YES YES YES YES NOGlucoside Bromosuccinic NO NO NO YES YES YES YES YES YES YES YES YES YESYES YES YES YES acid Citric acid YES YES YES YES YES YES NO NO YES YESYES YES YES YES YES YES YES D-Alanine YES YES YES YES YES YES YES YESYES YES NO YES YES YES YES YES YES D-Aspartic acid NO NO NO NO NO NO NONO NO NO NO NO NO NO NO NO NO D-Cellobiose YES YES YES YES YES YES YESNO YES YES YES YES YES YES YES YES YES D-Fructose YES YES YES YES YESYES YES YES YES YES YES YES YES YES YES YES YES D-Fructose-6- YES YESYES YES YES YES YES NO NO YES NO YES YES YES YES YES NO PhosphateD-Galactonic YES YES YES YES YES YES NO NO NO NO NO NO NO YES YES YESYES acid-g-Lactone D-Galactose YES YES YES YES YES YES YES YES NO YES NOYES YES YES YES YES YES D-Galacturonic YES YES YES YES YES YES YES NOYES YES YES YES NO YES YES YES NO acid D-Gluconic acid YES YES YES YESYES YES YES YES YES YES NO YES YES YES YES YES YES D-Glucosaminic YESYES YES NO YES YES NO NO YES YES NO YES NO YES YES YES YES acidD-Glucose-1- YES YES YES YES YES YES YES NO NO YES NO YES NO YES YES YESNO Phosphate D-Glucose-6- YES YES YES YES YES YES YES YES NO YES YES YESNO YES YES YES NO Phosphate D-Glucuronic YES YES YES YES YES YES YES NOYES YES NO YES YES YES YES YES YES acid D-Malic acid NO NO NO NO YES NONO YES YES YES NO YES NO YES YES YES YES D-Mannitol YES YES YES YES YESYES YES NO YES YES YES YES YES YES YES YES NO D-Mannose YES YES YES YESYES YES YES YES NO YES YES YES YES YES YES YES YES D-Melibiose YES YESYES YES YES YES YES NO NO YES NO YES YES YES YES YES NO D-Psicose YES NONO NO YES YES NO NO NO YES NO YES YES YES YES YES NO D-Ribose YES YESYES YES YES YES YES YES YES YES YES YES YES YES YES YES YES D-Saccharicacid YES YES YES YES YES YES YES YES NO YES YES YES NO YES YES YES NOD-Serine NO NO NO NO NO NO NO NO NO NO NO NO NO NO NO NO NO D-SorbitolYES YES YES YES YES NO NO NO NO NO NO NO YES YES YES YES NO D-ThreonineNO NO NO NO NO NO NO NO NO NO NO NO NO NO NO NO NO D-Trehalose YES YESYES YES YES YES YES YES YES YES YES YES YES YES YES YES YES D-Xylose YESYES YES YES YES YES YES YES YES YES NO YES YES YES YES YES YESDL-a-Glycerol YES YES YES YES YES YES YES YES YES YES NO YES YES YES YESYES NO Phosphate DL-Malic acid YES YES YES YES YES YES YES YES YES YESYES YES YES YES YES YES YES Dulcitol YES YES YES YES NO YES NO YES NOYES NO YES NO YES YES NO YES Formic acid YES YES YES NO YES YES NO NO NOYES YES YES NO YES YES YES NO Fumaric acid YES YES YES YES YES YES YESYES YES YES YES YES YES YES YES YES YES Glucuronamide NO NO NO YES NO NONO NO NO NO NO NO NO NO NO NO NO Gly-Asp NO YES YES YES NO YES YES NO NOYES NO YES NO YES YES NO YES Gly-Glu NO YES YES YES NO YES YES YES YESYES YES YES YES YES YES YES YES Gly-Pro NO YES YES YES YES YES YES NOYES YES YES YES YES YES YES YES YES Glycerol YES YES YES YES YES YES YESYES YES YES NO YES YES YES YES YES NO Glycolic acid NO NO NO NO YES NONO NO NO NO NO YES NO YES NO YES YES Glyoxylic acid NO YES YES NO NO NONO NO NO NO NO NO NO YES NO NO NO Inosine YES YES YES YES YES YES YES NOYES YES NO YES YES YES YES YES NO L-Alanine YES YES YES YES YES YES YESYES NO YES NO YES YES YES YES YES YES L-Arabinose YES YES YES YES YESYES YES YES YES YES YES YES YES YES YES YES YES L-Asparagine YES YES YESYES YES YES YES YES YES YES NO YES YES YES YES YES YES L-Aspartic acidYES YES YES YES YES YES YES YES YES YES YES YES YES YES YES YES YESL-Fucose NO NO NO NO YES NO NO NO YES NO NO YES YES YES YES YES YESL-Galactonic YES YES YES YES YES YES YES YES YES YES YES YES YES YES YESYES YES acid-g-Lactone L-Glutamic acid YES YES YES YES YES YES YES YESYES YES NO YES YES YES YES YES YES L-Glutamine YES YES YES YES YES YESYES YES YES YES YES YES YES YES YES YES YES L-Lactic acid YES YES YESYES YES YES YES YES YES YES YES YES YES YES YES YES YES L-Lyose NO NO NOYES YES YES YES YES NO NO YES NO YES YES YES NO NO L-Malic acid YES YESYES YES YES YES YES YES YES YES YES YES YES YES YES YES YES L-ProlineYES YES YES YES YES YES YES YES YES YES YES YES YES YES YES YES YESL-Rhamnose YES YES YES YES YES YES YES NO NO NO NO YES NO YES YES NO YESL-Serine YES YES YES YES YES YES YES NO YES YES NO YES YES YES YES YESYES L-Threonine NO NO NO YES YES NO NO NO NO YES NO NO YES YES YES NO NOLactulose NO NO NO NO YES YES YES NO YES YES YES YES YES YES YES YES NOm- NO YES YES YES NO NO YES NO YES YES NO YES YES YES YES YES NOHydroxyphenyl Acetic acid m-Inositol YES NO NO NO YES YES NO NO NO YESNO YES NO YES YES YES YES m-Tartaric acid YES NO NO NO YES YES NO NO NOYES NO YES NO YES YES YES NO Maltose YES YES YES YES YES YES YES NO YESYES YES YES NO YES YES YES YES Maltotriose YES YES YES YES YES YES YESNO YES YES YES YES YES YES YES YES YES Methylpyruvate YES YES YES YESYES YES YES YES YES YES YES YES YES YES YES YES YES Mono- NO NO NO NOYES NO NO YES YES YES NO YES YES YES YES YES NO Methylsuccinate Mucicacid YES YES YES YES YES YES NO YES NO YES NO YES NO YES YES YES NON-Acetyl-D- YES YES YES YES YES YES YES YES YES YES YES YES YES YES YESYES YES Glucosamine N-Acetyl-D- NO NO NO NO NO NO YES NO NO NO NO NO NONO YES NO NO Mannosamine Negative Control NO NO NO NO NO NO NO NO NO NONO NO NO NO NO NO NO p-Hydroxyphenyl NO YES YES YES YES NO YES NO YES NONO YES YES YES NO YES NO Acetic acid Phenylethylamine NO NO NO NO NO NONO NO NO NO NO NO NO YES NO YES NO Propionic acid NO NO NO NO YES NO NONO NO YES YES YES YES YES YES YES YES Pyruvic acid YES YES YES YES YESYES YES YES YES YES YES YES YES YES YES YES YES Succinic acid YES YESYES YES YES YES YES YES YES YES YES YES YES YES YES YES YES Sucrose YESYES YES YES YES YES YES NO YES YES YES YES YES YES YES YES YES ThymidineYES YES YES YES NO YES YES NO NO YES NO YES NO YES NO YES NOTricarballylic NO NO NO NO NO NO NO NO YES NO NO YES NO YES NO YES NOacid Tween 20 NO NO NO YES YES YES NO YES YES YES YES YES YES YES YESYES NO Tween 40 YES NO NO YES YES YES YES YES YES YES YES YES YES YESYES YES NO Tween 80 YES NO NO YES YES YES YES YES YES YES YES YES YESYES YES YES YES Tyramine NO NO NO NO NO NO NO NO NO NO NO NO NO YES NONO NO Uridine NO NO NO YES YES YES YES YES YES YES YES YES YES YES YESYES YES

TABLE W Substrate utilization as determined by BIOLOG PM1 MicroPlates byfungal endophytes belonging to OTUs present in cereal seeds, fruitseeds, vegetable seeds, and oil seeds. SYM- SYM- SYM- SYM- SYM- SYM-SYM- SYM- SYM- SYM- SYM- SYM- SYM- SYM- SYM- SYM- 00157 00300 0030100577 01314 01324 01326 01329 01330 01331 12462 15774 15783 15810 1587915880 1,2-Propanediol YES YES NO YES YES NO NO YES NO NO YES NO NO YESYES NO 2-Aminoethanol YES YES YES YES YES YES YES NO NO NO NO NO YES YESYES YES 2′- YES YES YES YES YES YES YES YES NO NO NO YES YES YES YES YESDeoxyadenosine a-D-Glucose YES YES YES YES YES YEgS YES YES YES YES YESYES YES YES YES YES a-D-Lactose YES YES YES YES YES YES YES YES YES YESYES YES YES YES YES YES a-Hydroxybutyric NO YES YES NO YES YES NO NO YESNO NO NO YES YES YES NO acid a-Hydroxyglutaric YES NO NO NO YES YES YESNO YES NO YES YES YES NO YES NO acid-g-Lactone a-Ketobutyric acid YESYES YES YES YES YES YES NO YES NO YES YES YES YES YES YES a-KetoglutaricYES YES YES YES YES YES YES YES YES YES YES NO YES YES YES YES acida-Methyl-D- YES YES YES YES YES YES YES YES NO YES YES YES YES YES YESYES Galactoside Acetic acid YES YES YES YES YES YES YES YES NO YES YESNO YES YES YES YES Acetoacetic acid YES NO YES NO YES NO YES NO NO NOYES YES YES NO YES NO Adenosine YES YES YES YES YES YES YES NO NO YESYES NO YES YES YES YES Adonitol YES YES YES YES YES YES YES YES NO YESYES YES YES YES YES YES Ala-Gly YES YES YES YES YES YES YES YES YES YESYES YES YES YES YES YES b-Methyl-D- YES YES YES YES YES YES YES YES YESYES YES YES YES YES YES YES Glucoside Bromosuccinic YES YES YES YES YESYES YES NO YES YES YES YES YES YES YES YES acid Citric acid YES YES YESYES YES YES YES YES YES NO YES NO YES NO YES YES D-Alanine YES YES YESYES YES NO YES NO NO NO NO NO NO YES YES YES D-Aspartic acid NO YES NONO YES YES YES YES NO YES YES YES YES YES YES NO D-Cellobiose YES YESYES YES YES YES YES YES YES YES YES YES YES YES YES YES D-Fructose YESYES YES YES YES YES YES YES YES YES YES YES YES YES YES YESD-Fructose-6- NO YES NO NO YES NO YES YES YES NO NO YES NO YES YES NOPhosphate D-Galactonic NO NO NO NO NO NO NO NO NO NO YES NO NO NO YES NOacid-g-Lactone D-Galactose YES YES YES YES YES YES YES YES YES YES YESYES YES YES YES YES D-Galacturonic YES YES YES YES YES YES YES YES YESYES YES YES YES YES YES YES acid D-Gluconic acid YES NO YES NO YES YESYES YES YES YES YES YES YES YES YES YES D-Glucosaminic YES YES YES YESYES YES YES YES NO NO YES YES YES NO NO NO acid D-Glucose-1- NO YES NONO NO NO NO NO YES NO YES YES NO NO NO NO Phosphate D-Glucose-6- NO YESNO NO YES NO YES NO YES NO YES YES YES YES YES NO Phosphate D-GlucuronicYES YES YES YES YES YES YES YES YES YES YES YES YES YES YES YES acidD-Malic acid NO YES YES YES YES YES YES YES NO YES NO NO YES YES YES YESD-Mannitol YES YES YES YES YES YES YES YES YES YES YES NO YES YES YESYES D-Mannose YES YES YES YES YES YES YES YES YES YES YES YES YES YESYES YES D-Melibiose YES YES YES YES YES YES YES YES YES YES YES YES YESYES YES YES D-Psicose YES YES YES NO NO YES YES YES NO YES NO NO YES YESYES YES D-Ribose YES YES YES YES YES YES YES YES YES YES YES YES YES YESYES YES D-Saccharic acid YES YES YES NO YES YES NO YES YES YES YES NOYES YES YES YES D-Serine YES YES YES YES YES YES YES NO NO NO NO NO YESYES YES NO D-Sorbitol YES YES YES YES YES YES YES YES YES YES YES NO YESYES YES YES D-Threonine YES NO NO NO YES NO YES YES NO YES YES YES YESNO YES NO D-Trehalose YES YES YES YES YES YES YES YES YES YES YES YESYES YES YES YES D-Xylose YES YES YES YES YES YES YES NO YES YES YES NOYES YES YES YES DL-a-Glycerol NO NO NO NO YES NO YES NO YES NO NO YESYES YES YES YES Phosphate DL-Malic acid YES YES YES YES YES YES YES YESNO YES YES YES YES YES YES YES Dulcitol YES YES YES YES YES YES YES YESNO YES YES NO YES YES YES YES Formic acid YES NO YES NO YES YES YES NONO NO NO YES NO YES YES NO Fumaric acid YES YES YES YES YES YES YES YESNO YES YES YES YES YES YES YES Glucuronamide NO NO NO NO NO NO YES NO NONO NO NO NO NO YES NO Gly-Asp YES YES YES YES YES YES YES YES NO YES YESYES YES YES YES YES Gly-Glu YES YES YES YES YES YES YES YES YES YES YESYES YES YES YES YES Gly-Pro YES YES YES YES YES YES YES YES YES YES YESYES YES YES YES YES Glycerol YES YES YES YES YES YES YES NO YES NO YESYES YES YES YES YES Glycolic acid NO NO NO NO YES YES NO NO YES NO NOYES YES YES NO YES Glyoxylic acid YES NO NO NO YES YES NO NO NO NO YESNO YES YES YES YES Inosine YES YES YES NO YES YES YES NO NO YES YES NONO YES YES YES L-Alanine YES YES YES YES YES YES YES YES YES YES YES YESYES YES YES YES L-Arabinose YES YES YES YES YES YES YES YES YES YES YESNO YES YES YES YES L-Asparagine YES YES YES YES YES YES YES NO YES YESYES YES YES YES YES YES L-Aspartic acid YES YES YES YES YES YES YES NONO YES YES YES YES YES YES YES L-Fucose YES YES YES YES YES YES YES YESYES YES NO YES NO YES YES NO L-Galactonic YES YES YES YES YES YES YESYES YES YES YES YES YES YES YES YES acid-g-Lactone L-Glutamic acid YESYES YES YES YES YES YES YES NO YES YES YES YES YES YES YES L-GlutamineYES YES YES YES YES YES YES YES YES YES YES YES YES YES YES YES L-Lacticacid YES YES YES YES YES YES YES NO NO YES YES YES YES YES YES YESL-Lyxose YES YES YES YES YES NO YES NO YES YES NO NO YES YES YES YESL-Malic acid YES YES YES YES YES YES YES YES YES YES YES YES YES YES YESYES L-Proline YES YES YES YES YES YES YES YES YES YES YES NO YES YES YESYES L-Rhamnose YES YES YES YES YES YES YES YES YES YES YES YES YES YESYES YES L-Serine YES YES YES YES YES YES YES YES YES YES YES YES YES YESYES YES L-Threonine YES YES YES YES YES YES YES YES NO NO YES YES YESYES YES YES Lactulose YES YES YES YES YES YES YES YES NO YES YES YES YESYES YES NO m-Hydroxyphenyl YES YES YES NO YES YES NO YES NO NO YES YESYES NO NO YES Acetic acid m-Inositol YES YES YES YES YES YES YES YES NOYES YES YES YES YES YES YES m-Tartaric acid YES YES YES NO YES YES YESYES NO YES NO NO YES YES YES NO Maltose YES YES YES YES YES YES YES YESYES YES YES YES YES YES YES YES Maltotriose YES YES YES YES YES YES YESYES YES YES YES YES YES YES YES YES Methylpyruvate YES YES YES YES YESYES YES NO YES YES YES YES YES YES YES YES Mono- YES YES YES YES YES YESYES NO YES YES YES YES YES YES YES YES Methylsuccinate Mucic acid YESYES YES NO YES YES NO YES NO YES YES YES YES YES YES YES N-Acetyl-D- YESYES YES YES YES YES YES YES YES YES YES YES YES YES YES YES GlucosamineN-Acetyl-D- NO YES NO NO YES NO YES NO YES NO NO YES YES NO NO NOMannosamine Negative Control NO NO NO NO NO NO NO NO NO NO NO NO NO NONO NO p-Hydroxyphenyl YES NO YES YES YES YES NO NO YES YES YES NO YESYES YES YES Acetic acid Phenylethylamine NO NO NO NO YES NO YES NO NO NONO NO NO NO NO YES Propionic acid YES YES YES YES YES YES YES NO NO NOYES YES YES YES YES YES Pyruvic acid YES YES YES YES YES YES YES YES NOYES YES YES YES YES YES YES Succinic acid YES YES YES YES YES YES YESYES NO YES YES YES YES YES YES YES Sucrose YES YES YES YES YES YES YESYES YES YES YES YES YES YES YES YES Thymidine YES NO NO NO NO YES YES NONO NO YES NO NO YES YES NO Tricarballylic NO NO YES YES YES YES NO NO NONO NO YES YES YES NO NO acid Tween 20 YES YES YES YES YES YES YES NO YESYES YES YES YES YES YES YES Tween 40 YES YES YES YES YES YES YES YES YESYES YES YES YES YES YES YES Tween 80 YES YES YES YES YES YES YES YES YESYES YES YES YES YES YES YES Tyramine YES YES YES YES YES YES YES YES NOYES YES NO YES YES YES YES Uridine YES NO YES YES YES NO YES YES NO NONO NO NO YES YES YES

TABLE X Substrate utilization as determined by BIOLOG PM2 MicroPlates bybacterial endophytes belonging to OTUs present in cereal seeds, fruitseeds, vegetable seeds, and oil seeds. SYM- SYM- SYM- SYM- SYM- SYM-SYM- SYM- SYM- SYM- SYM- SYM- SYM- SYM- SYM- SYM- SYM- Strain/Substrate00021b 00044 00057b 00074 00091 00092d 00212 00290 00619 00865 0087900879b 00906 00965 01004 01022 01158 2-Deoxy-D- NO YES YES YES YES NOYES YES YES YES YES YES YES YES NO YES YES Ribose 2-Hydroxybenzoic NO NONO NO NO NO NO NO NO NO NO NO NO NO NO NO NO acid 2,3-Butanediol YES NONO NO NO NO NO NO NO NO NO YES NO YES YES NO YES 2,3-Butanedione NO NONO NO NO NO NO NO NO NO NO NO NO NO NO NO NO 3-Hydroxy-2- NO NO NO YESNO NO NO NO NO NO NO NO NO NO NO YES YES butanone 3-Methylglucose NO NONO NO NO YES NO NO NO NO NO YES NO YES YES YES YES 3-O-b-D- YES YES YESYES YES YES NO YES NO YES YES YES YES YES YES YES YES Galactopyranosyl-D-Arabinose 4-Hydroxybenzoic NO NO NO NO YES NO NO NO NO NO NO NO NO NOYES NO YES acid 5-Keto-D- YES YES YES NO NO YES YES YES NO YES YES YESNO YES YES YES YES Gluconic acid a-Cyclodextrin NO NO NO YES YES YES NONO YES YES NO YES NO YES YES YES NO a-Keto-Valeric NO NO NO NO NO NO NOYES NO NO NO NO NO YES NO YES YES acid a-Methyl-D- NO NO NO NO YES YESNO NO YES NO NO NO YES YES YES YES YES Glucoside a-Methyl-D- NO NO NO NONO NO NO NO NO NO NO YES NO NO NO NO NO Mannoside Acetamide YES NO NO NONO NO NO NO NO NO YES NO NO YES NO NO NO Amygdalin YES YES YES YES YESYES NO YES YES YES YES YES YES YES YES YES YES Arbutin YES YES YES YESYES YES YES NO NO YES YES YES YES YES YES YES YES b-Cyclodextrin NO NONO NO YES YES NO YES YES NO NO YES NO YES YES YES NO b-D-Allose NO NO NONO NO NO NO NO NO NO NO NO NO YES NO NO NO b-Hydroxybutyric YES NO NO NOYES NO NO YES NO NO YES YES YES YES YES YES YES acid b-Methyl-D- YES YESYES YES YES YES YES NO YES YES YES YES YES YES YES YES YES Galactosideb-Methyl-D- NO NO NO YES NO NO NO NO NO NO NO NO NO NO NO YES YESGlucuronic acid b-Methyl-D- NO NO NO NO NO NO NO NO NO NO NO YES NO YESYES NO YES Xyloside Butyric acid NO NO NO YES NO NO NO YES NO YES YESYES YES YES YES YES YES Capric acid NO NO NO NO NO NO NO NO NO NO NO NONO NO NO NO NO Caproic acid NO NO NO NO NO NO NO YES NO NO NO NO NO NONO NO YES Chondroitin YES NO NO YES YES NO NO NO NO YES YES YES YES YESNO YES YES Sulfate C Citraconic acid NO NO NO NO NO YES NO NO NO NO NOYES NO YES YES NO YES Citramalic acid YES NO NO NO NO NO NO NO NO NO NOYES NO YES YES YES YES d-Amino Valeric NO NO NO NO YES NO NO NO NO NO NONO NO YES NO YES YES acid D-Arabinose NO NO NO NO YES YES YES YES NO NOYES YES YES YES YES NO YES D-Arabitol YES YES YES YES YES YES YES NO YESYES NO YES NO YES YES YES YES D-Fucose YES YES YES NO YES YES NO NO NONO NO NO NO YES YES NO YES D-Glucosamine YES YES YES YES YES YES YES YESYES YES YES YES YES YES YES YES YES D-Lactic acid NO NO NO YES NO NO NOYES NO YES YES NO NO NO YES YES YES Methyl Ester D-Lactitol NO NO NO YESYES NO NO NO NO YES YES NO YES YES YES YES YES D-Melezitose NO NO NO NONO NO YES NO NO NO NO YES YES YES YES YES YES D-Raffinose YES YES YESYES YES NO YES NO NO YES NO YES YES YES YES YES YES D-Ribono-1,4- YES NONO NO NO YES NO NO NO NO NO YES YES YES YES NO YES Lactone D-Tagatose NONO NO NO NO NO NO NO NO YES NO YES NO YES YES NO YES D-Tartaric acid YESNO NO YES NO NO NO NO NO NO NO NO NO NO YES NO YES D,L-Carnitine NO NONO NO YES NO NO NO NO NO NO NO NO YES YES NO YES D,L-Octopamine NO NO NONO NO NO NO NO NO NO NO NO NO NO NO YES NO Dextrin YES YES YES YES YESYES YES YES YES YES YES YES YES YES YES YES YES Dihydroxyacetone NO NONO YES YES YES YES YES YES YES YES YES YES YES YES YES YES g-Amino-N-YES NO NO NO YES YES NO NO NO YES NO YES NO YES YES YES YES Butyric acidg-Cyclodextrin NO NO NO NO NO NO NO NO NO YES NO YES NO YES NO YES YESg-Hydroxybutyric NO NO NO NO NO NO NO NO NO NO YES YES NO YES YES YESYES acid Gelatin NO NO NO YES YES NO NO YES NO YES YES YES YES YES YESYES YES Gentiobiose YES YES YES YES YES YES YES NO YES YES YES YES YESYES YES YES YES Glycine NO NO NO YES NO NO NO NO NO NO NO NO NO YES NOYES YES Glycogen NO YES YES YES NO YES YES YES YES YES NO YES YES YESYES YES YES Hydroxy-L- NO NO NO NO YES NO NO NO NO YES NO YES NO YES YESYES YES Proline i-Erythritol YES NO NO NO YES YES YES NO NO NO YES NO NOYES YES NO YES Inulin NO NO NO NO NO NO NO NO NO YES NO NO NO NO NO YESYES Itaconic acid NO NO NO NO YES NO NO NO NO NO NO YES YES YES NO YESYES L-Alaninamide YES NO NO YES YES YES NO YES NO YES YES YES YES YES NOYES YES L-Arabitol NO NO NO NO YES YES NO NO NO NO NO YES NO YES YES NOYES L-Arginine YES YES YES YES YES YES NO NO NO YES NO YES NO YES YESYES YES L-Glucose NO NO NO NO NO NO NO NO NO NO NO NO NO NO NO NO NOL-Histidine YES NO NO YES YES YES YES NO NO YES NO YES YES YES YES YESYES L-Homoserine NO NO NO NO NO NO NO NO NO NO NO NO NO YES NO YES NOL-Isoleucine NO NO NO NO YES NO NO NO NO YES NO YES YES YES YES YES YESL-Leucine YES NO NO NO NO NO NO NO NO YES YES YES YES YES YES YES YESL-Lysine NO NO NO NO YES NO NO NO NO YES NO YES NO YES YES YES YESL-Methionine NO NO NO NO NO YES NO NO NO NO NO NO NO NO NO NO NOL-Ornithine YES YES YES YES YES YES YES YES NO YES NO YES YES YES YESYES YES L-Phenylalanine YES NO NO YES NO NO YES NO NO YES NO YES YES YESNO YES NO L-Pyroglutamic YES NO NO YES NO YES NO NO NO NO NO YES YES YESYES YES YES acid L-Sorbose NO NO NO NO NO NO NO NO NO NO NO NO NO NO NONO NO L-Tartaric acid YES YES YES NO NO YES YES NO NO NO YES NO NO NO NOYES YES L-Valine NO NO NO NO NO NO NO NO NO YES NO YES YES YES NO YESYES Laminarin NO NO NO NO YES NO NO YES NO YES YES YES YES YES YES YESYES Malonic acid YES NO NO YES NO NO YES NO NO YES YES NO YES YES YES NOYES Maltitol YES NO NO NO YES NO NO NO NO YES YES NO YES YES YES YES YESMannan NO NO NO YES NO YES YES YES NO NO NO NO YES YES YES NO YESMelibionic acid YES YES YES YES YES NO NO YES NO YES NO YES NO YES YESYES YES N-Acetyl-D- YES NO NO NO NO NO NO NO NO YES YES YES YES YES YESYES YES Galactosamine N-Acetyl-D- NO NO NO NO NO NO NO NO NO NO NO NO NONO NO NO YES Glucosaminitol N-Acetyl-L- NO NO NO YES NO YES NO NO NO YESNO YES YES YES NO YES YES Glutamic acid N-Acetyl- NO YES YES YES NO NOYES NO NO NO NO YES YES YES NO NO YES Neuraminic acid Negative NO NO NONO NO NO NO NO NO NO NO NO NO NO NO NO NO Control.1 Oxalic acid NO NO NONO NO NO NO NO NO NO YES NO NO NO YES NO NO Oxalomalic acid NO NO NO NOYES YES NO YES NO YES YES YES YES YES YES YES YES Palatinose YES NO NONO YES NO NO NO YES YES YES YES YES YES YES YES YES Pectin YES YES YESYES YES YES YES YES NO YES YES YES YES YES YES YES YES Putrescine YES NONO YES NO NO NO NO NO NO NO YES YES YES YES YES YES Quinic acid YES NONO NO YES YES NO NO NO YES NO YES NO YES YES YES YES Salicin YES YES YESYES YES YES YES NO YES YES YES YES YES YES YES YES YES Sebacic acid YESNO NO NO NO NO NO YES YES NO NO YES NO YES NO YES YES sec-Butylamine NONO NO NO NO NO NO NO NO NO NO NO NO NO NO NO NO Sedoheptulosan NO NO NONO NO NO NO NO NO NO NO NO NO NO NO NO NO Sorbic acid NO NO NO NO NO NONO YES NO YES NO YES YES YES NO YES YES Stachyose NO NO NO NO YES NO NONO NO NO NO NO NO YES YES YES YES Succinamic acid YES YES YES YES YESYES YES YES NO YES YES YES YES YES YES YES YES Turanose YES NO NO NO YESYES NO NO YES YES YES YES YES YES YES YES YES Xylitol NO NO NO NO YES NONO NO NO NO NO YES NO YES YES NO NO

TABLE Y Substrate utilization as determined by BIOLOG PM2 MicroPlates byfungal endophytes belonging to OTUs present in cereal seeds, fruitseeds, vegetable seeds, and oil seeds. SYM- SYM- SYM- SYM- SYM- SYM-SYM- SYM- SYM- SYM- SYM- SYM- SYM- SYM- SYM- SYM- Strain/Substrate 0015700300 00301 00577 01314 01324 01326 01329 01330 01331 12462 15774 1578315810 15879 15880 2-Deoxy-D- YES NO NO NO YES NO NO NO NO NO NO NO YESYES YES NO Ribose 2-Hydroxybenzoic YES YES YES YES YES YES YES NO YESYES YES YES YES YES YES YES acid 2,3-Butanediol NO NO YES NO NO YES NONO YES YES NO YES NO YES NO NO 2,3-Butanedione NO NO YES NO NO YES NO NOYES YES NO NO NO YES NO NO 3-Hydroxy-2- NO NO NO NO NO YES NO NO YES NONO NO NO NO NO NO butanone 3-Methylglucose YES NO YES YES NO NO NO YESYES YES NO NO YES NO YES NO 3-O-b-D- YES YES YES YES YES YES NO YES NOYES YES YES YES YES NO YES Galactopyranosyl- D-Arabinose 4- YES YES YESYES YES YES YES YES YES YES NO YES YES YES YES YES Hydroxybenzoic acid5-Keto-D- NO NO YES NO YES YES YES NO YES YES YES YES YES YES YES YESGluconic acid a-Cyclodextrin YES YES YES YES YES YES YES YES YES YES YESYES YES YES YES YES a-Keto-Valeric YES YES YES YES YES YES YES YES YESYES YES YES YES YES YES YES acid a-Methyl-D- YES YES YES YES YES YES YESYES YES YES NO YES YES YES YES YES Glucoside a-Methyl-D- YES NO YES NONO YES YES NO YES YES NO NO YES YES YES NO Mannoside Acetamide YES YESYES NO NO NO NO NO YES YES NO YES NO NO NO NO Amygdalin YES YES YES YESYES YES YES YES YES YES YES YES YES YES YES YES Arbutin YES YES YES YESYES YES YES YES YES YES YES YES YES YES YES YES b-Cyclodextrin YES YESYES NO NO YES YES NO NO YES YES YES YES YES YES YES b-D-Allose NO NO YESNO NO NO YES NO NO NO NO YES YES YES YES YES b-Hydroxybutyric YES YESYES YES YES YES YES YES YES YES YES YES YES YES YES NO acid b-Methyl-D-YES YES YES YES YES YES YES YES YES YES YES YES YES YES YES YESGalactoside b-Methyl-D- YES NO NO NO YES NO NO NO YES NO NO NO NO NO YESNO Glucuronic acid b-Methyl-D- NO NO YES NO YES YES YES NO NO NO NO NOYES YES NO NO Xyloside Butyric acid YES YES YES YES YES YES YES YES YESYES NO NO YES YES YES YES Capric acid NO NO NO NO NO NO NO NO NO NO NONO NO NO NO NO Caproic acid NO YES YES YES YES YES YES NO NO YES NO NOYES YES YES YES Chondroitin YES NO YES NO YES YES NO NO YES YES YES NONO YES YES NO Sulfate C Citraconic acid YES NO YES NO YES YES NO NO YESYES YES NO YES YES NO NO Citramalic acid YES NO NO NO YES YES NO YES YESYES NO NO YES YES YES YES d-Amino Valeric NO YES YES YES YES YES YES NOYES YES YES NO YES YES YES YES acid D-Arabinose YES YES YES YES YES YESYES YES NO YES YES YES YES YES YES YES D-Arabitol YES YES YES YES YESYES YES YES YES YES YES YES YES YES YES YES D-Fucose YES NO YES NO YESYES NO NO NO YES NO YES YES YES YES YES D-Glucosamine YES YES YES YESYES YES YES NO YES YES NO NO NO YES YES YES D-Lactic acid YES NO YES NONO NO NO NO YES NO YES NO NO YES NO NO Methyl Ester D-Lactitol YES YESYES YES NO NO YES YES NO YES YES YES YES YES YES NO D-Melezitose YES YESYES YES YES YES YES YES YES YES YES YES YES YES YES YES D-Raffinose YESYES YES YES YES YES YES YES YES YES YES YES YES YES YES YESD-Ribono-1,4- YES NO YES YES YES NO YES NO YES YES NO NO YES NO NO YESLactone D-Tasatose NO YES YES NO YES NO YES NO YES NO NO NO YES YES YESYES D-Tartaric acid YES NO NO NO YES NO NO NO YES NO NO YES YES NO YESNO D,L-Carnitine YES NO YES NO NO NO NO NO YES YES YES NO NO NO NO NOD,L-Octopamine YES NO YES NO YES YES NO NO NO YES NO YES YES YES YES NODextrin YES YES YES YES YES YES YES YES YES YES YES YES YES YES YES YESDihydroxyacetone YES YES YES YES YES YES YES NO YES YES NO NO YES YESYES NO g-Amino-N- YES YES YES YES YES YES YES YES YES YES YES NO YES YESYES YES Butyric acid g-Cyclodextrin YES YES YES YES YES YES YES YES YESYES YES YES YES YES YES YES g-Hydroxybutyric YES YES YES YES YES YES YESYES YES YES YES YES YES YES NO NO acid Gelatin YES YES YES YES YES YESYES YES YES YES YES YES YES YES YES NO Gentiobiose YES YES YES YES YESYES YES YES YES YES YES YES YES YES YES YES Glycine YES YES YES YES YESYES YES NO YES YES YES NO YES YES YES YES Glycogen YES YES YES YES YESYES YES YES YES YES YES YES YES YES YES YES Hydroxy-L- YES YES YES YESYES YES YES NO YES YES YES NO YES YES YES YES Proline i-Erythritol YESYES YES YES YES YES YES YES YES YES YES NO YES YES NO YES Inulin YES YESYES YES YES NO NO NO YES NO YES YES NO YES YES YES Itaconic acid NO NOYES NO NO NO NO YES NO YES NO NO NO NO NO NO L-Alaninamide YES YES YESYES YES YES YES YES YES YES YES YES YES YES YES NO L-Arabitol YES YESYES YES YES YES YES YES YES YES YES NO YES YES YES YES L-Arginine YESYES YES YES YES YES YES YES YES YES YES YES YES YES YES YES L-Glucose NONO YES NO NO NO YES NO NO YES NO NO YES YES YES NO L-Histidine YES YESYES YES YES YES YES NO YES NO YES YES YES YES YES YES L-Homoserine YESYES YES YES NO YES YES NO NO YES NO NO YES NO YES NO L-Isoleucine YESYES YES YES YES YES YES YES YES YES YES YES YES YES YES YES L-LeucineYES YES YES YES YES YES YES NO YES YES NO YES YES YES YES NO L-LysineYES YES YES YES YES YES YES NO YES YES YES YES YES YES YES YESL-Methionine NO NO NO NO NO NO NO NO NO NO NO YES YES NO NO NOL-Ornithine YES YES YES YES YES YES YES YES YES YES YES YES YES YES YESYES L-Phenylalanine YES YES YES YES YES YES YES NO YES YES YES YES YESYES YES YES L-Pyroglutamic YES YES YES YES YES YES YES YES YES YES YESYES NO YES YES YES acid L-Sorbose NO YES YES YES YES YES YES NO YES NOYES NO YES YES YES YES L-Tartaric acid YES NO YES NO YES YES YES YES NOYES NO YES NO YES YES NO L-Valine YES YES YES YES YES YES YES YES YESYES NO NO YES YES YES YES Laminarin YES YES YES YES YES YES YES NO NOYES YES YES YES YES YES NO Malonic acid YES NO YES YES YES YES YES NOYES YES NO YES YES YES YES NO Maltitol YES YES YES YES YES YES YES YESYES YES NO YES YES YES YES YES Mannan YES NO YES NO YES NO NO NO YES NOYES YES NO NO NO NO Melibionic acid YES NO YES YES YES YES YES NO YESYES YES YES NO YES YES NO N-Acetyl-D- YES NO NO NO NO NO YES NO YES NONO YES NO YES NO NO Galactosamine N-Acetyl-D- NO NO NO NO YES YES NO YESNO NO NO NO NO YES YES NO Glucosaminitol N-Acetyl-L- NO NO YES NO NO YESNO NO YES YES NO YES NO NO NO NO Glutamic acid N-Acetyl- NO NO NO NO NONO NO NO NO NO NO NO NO NO NO NO Neuraminic acid Negative NO NO NO NO NONO NO NO NO NO NO NO NO NO NO NO Control.1 Oxalic acid YES YES YES YESYES YES YES NO YES YES YES NO YES YES YES NO Oxalomalic acid NO NO NO NOYES NO NO NO YES NO NO NO YES YES YES NO Palatinose YES YES YES YES YESYES YES YES YES YES YES YES YES YES YES YES Pectin YES NO YES NO YES YESYES YES YES YES YES YES YES YES YES YES Putrescine YES YES YES YES YESYES YES YES YES YES YES NO YES YES YES YES Quinic acid YES YES YES YESYES YES YES YES YES YES NO YES YES YES YES YES Salicin YES YES YES YESYES YES YES YES YES YES YES YES YES YES YES YES Sebacic acid YES YES YESYES YES YES YES NO YES YES YES NO YES YES YES YES sec-Butylamine NO YESYES NO NO NO NO NO NO NO NO NO NO NO NO NO Sedoheptulosan YES YES NO NOYES YES YES YES YES YES YES YES YES YES YES YES Sorbic acid YES YES YESYES YES YES YES NO YES YES NO NO YES YES YES NO Stachyose YES YES YESYES YES YES YES YES YES YES YES YES YES YES YES YES Succinamic acid YESYES YES YES YES YES NO YES YES YES YES YES YES YES YES NO Turanose YESYES YES YES YES YES YES YES YES YES YES YES YES YES YES YES Xylitol YESYES YES YES YES YES YES YES YES YES YES YES YES YES YES YES

Seventeen (17) bacterial SYM strains and sixteen (16) fungal SYM strainswere tested in biological triplicate for sole carbon substrateutilization using BIOLOG PM1 and PM2A MicroPlates. The most utilizedsubstrates overall by these strains are a-D-Glucose, Arbutin,b-Methyl-D-Galactoside, b-Methyl-D-Glucoside, D-Arabitol, D-Cellobiose,Dextrin, D-Fructose, D-Galactose, D-Gluconic acid, D-Glucosamine,Dihydroxyacetone, DL-Malic acid, D-Mannitol, D-Mannose, D-Melezitose,D-Melibiose, D-Raffinose, D-Ribose, D-Trehalose, D-Xylose,g-Amino-N-Butyric acid, g-Cyclodextrin, Gelatin, Gentiobiose, Glycogen,i-Erythritol, L-Alanine, L-Arabinose, L-Galactonic acid-g-Lactone,L-Histidine, L-Proline, L-Rhamnose, Maltitol, Maltose, Maltotriose,N-Acetyl-D-Glucosamine, Palatinose, Pectin, Salicin, Stachyose, Sucrose,and Turanose. Overall, these strains did not utilize 2,3-Butanediol,2,3-Butanedione, b-Methyl-D-Glucuronic acid, b-Methyl-D-Xyloside, Capricacid, D,L-Carnitine, Glucuronamide, Itaconic acid, L-Methionine,N-Acetyl-D-Glucosaminitol, N-Acetyl-Neuraminic acid, Phenylethylamine,or sec-Butylamine as sole carbon sources.

The most utilized substrates by these seventeen bacterial endophytes are2-Deoxy-D-Ribose, a-D-Glucose, a-Methyl-D-Galactoside, Arbutin,b-Methyl-D-Galactoside, b-Methyl-D-Glucoside, D-Arabitol, D-Cellobiose,Dextrin, D-Fructose, D-Galactose, D-Galacturonic acid, D-Gluconic acid,D-Glucosamine, Dihydroxyacetone, DL-Malic acid, D-Mannitol, D-Mannose,D-Melibiose, D-Raffinose, D-Ribose, D-Trehalose, D-Xylose, Gelatin,Gentiobiose, L-Arabinose, L-Aspartic acid, L-Galactonic acid-g-Lactone,L-Glutamic acid, L-Glutamine, L-Histidine, L-Ornithine, L-Proline,Maltose, Maltotriose, N-Acetyl-D-Glucosamine, Pyruvic acid, Salicin,Sucrose, and Turanose. These bacterial endophytes did not utilize1,2-Propanediol, 2,3-Butanediol, 2,3-Butanedione, 2-Aminoethanol,2-Hydroxybenzoic acid, 3-Hydroxy-2-butanone, 3-Methylglucose,4-Hydroxybenzoic acid, Acetamide, Acetoacetic acid, a-Hydroxybutyricacid, a-Hydroxyglutaric acid-g-Lactone, a-Ketobutyric acid,a-Keto-Valeric acid, a-Methyl-D-Glucoside, a-Methyl-D-Mannoside,b-D-Allose, b-Methyl-D-Glucuronic acid, b-Methyl-D-Xyloside, Capricacid, Caproic acid, Citraconic acid, Citramalic acid, D,L-Carnitine,D,L-Octopamine, d-Amino Valeric acid, D-Aspartic acid, D-Melezitose,D-Serine, D-Tagatose, D-Tartaric acid, D-Threonine, g-Cyclodextrin,g-Hydroxybutyric acid, Glucuronamide, Glycine, Glycolic acid, Glyoxylicacid, Hydroxy-L-Proline, i-Erythritol, Inulin, Itaconic acid,L-Arabitol, L-Fucose, L-Glucose, L-Homoserine, L-Methionine, L-Sorbose,L-Threonine, L-Valine, m-Tartaric acid, N-Acetyl-D-Glucosaminitol,N-Acetyl-D-Mannosamine, N-Acetyl-Neuraminic acid, Oxalic acid,Phenylethylamine, Sebacic acid, sec-Butylamine, Sedoheptulosan,Stachyose, Tricarballylic acid, Tyramine, or Xylitol as sole carbonsources.

The most utilized substrates by these sixteen fungal endophytes area-D-Glucose, a-Methyl-D-Glucoside, Amygdalin, Arbutin,b-Methyl-D-Galactoside, b-Methyl-D-Glucoside, D-Arabitol, D-Cellobiose,Dextrin, D-Fructose, D-Galactose, D-Mannitol, D-Mannose, D-Melezitose,D-Melibiose, D-Raffinose, D-Trehalose, D-Xylose, g-Amino-N-Butyric acid,g-Cyclodextrin, Gentiobiose, Glycogen, i-Erythritol, L-Alanine,L-Arabinose, L-Arginine, L-Ornithine, L-Rhamnose, Maltitol, Maltose,Maltotriose, N-Acetyl-D-Glucosamine, Palatinose, Pectin, Putrescine,Quinic acid, Salicin, Stachyose, Sucrose, and Turanose. These fungalendophytes did not utilize 2,3-Butanediol, 2,3-Butanedione,2-Deoxy-D-Ribose, b-Methyl-D-Glucuronic acid, b-Methyl-D-Xyloside,Capric acid, D,L-Carnitine, D-Galactonic acid-g-Lactone,D-Glucose-1-Phosphate, Glucuronamide, Itaconic acid, L-Methionine,N-Acetyl-D-Galactosamine, N-Acetyl-D-Glucosaminitol, N-Acetyl-L-Glutamicacid, N-Acetyl-Neuraminic acid, Phenylethylamine, or sec-Butylamine assole carbon sources.

Example 5: Transcriptomic Characterization of Host Plant Response toSynthetic Compositions Comprising Plant Seeds and an Endophyte (SoyRNA-SEQ Experiments)

This Example describes the ability of synthetic compositions comprisingplant seeds a single endophyte strain or a plurality of endophytestrains described herein, to confer beneficial traits to a host plant.Among other things, this Example describe the ability of endophytes(e.g., endophytes described herein) to confer beneficial traits on avariety of host plants by modulating the transcriptome of the hostplant. In some embodiments, host plants include, but are not limited to,dicots (e.g., soy, peanuts) and monocots (e.g., plants described herein,e.g., corn, soy, wheat, cotton, sorghum), and combinations thereof.

Among other things, this Example describes surprising and unexpectedmodulations in the transcriptome of a host plant in response tosynthetic compositions comprising plant seeds and a beneficial fungalendophyte strain, compared to a neutral fungal strain of the same genus.

Plant Seedling

Untreated soy seeds were surface sterilized using chlorine fumes.Briefly, Erlenmyer flasks containing seeds and a bottle with 100 mL offresh bleach solution were placed in a desiccation jar located in a fumehood. Immediately prior to closing the lid of the desiccation jar, 3 mLhydrochloric acid was carefully pipetted into the bleach. Sterilizationwas done for 17 hours, and upon completion the flasks with seeds wereremoved, sealed in sterile foil, and opened in a sterile biosafetycabinet or laminar flow hood for subsequent work.

Soy Seedling Assay

Seeds were first coated with 3% sodium alginate, and gently shaken toobtain homogenous coverage. SYM strain fungal inoculum grown asdescribed previously was added to the sodium alginate coated seeds andgently mixed. For every one gram of seeds, 10 μL of sodium alginate andinoculum were applied. Formulation only soybean seeds were coated with3% sodium alginate and fresh PDB.

Ten seeds were placed on a 150 mm Petri plate that contained a singleheavy germination paper (SD5-¼ 76# heavy weight seed germination paper,Anchor Paper Co., St. Paul, Minn.) added with 10 mL 8% polyethyleneglycol (PEG 6000). Plates were incubated at 22° Celsius in dark and 60%relative humidity for five days. Seedlings were harvested at the end ofthe incubation period and stored in −80° C. until total RNA isolationusing standard extraction method using TriReagent (Sigma-Aldrich, St.Louis, Mo., USA) and purification with RNeasy Mini Kit (Qiagen, Hilden,Germany). All experiments (beneficial, neural, formulation) were done intriplicate under sterile conditions resulting in a total of ninesamples.

Soy RNA-SEQ

Initial quality control was performed using Agilent Bioanalyzer andTapestation.

polyA cDNA Preparation

For each of the 9 soybean RNAs, polyA cDNA was prepared using a ClontechcDNA synthesis kit. Briefly, after initial QC passed, 500 ng of totalRNA was used to generate 1-2 ug of cDNA using Clontech SMARTer PCR cDNAkit (Clontech Laboratories, Inc., Mountain View, Calif. USA, catalog#634925). Manufacturer's instructions were strictly followed to performpolyA cDNA construction; 14 PCR cycles were performed.

Fragmentation

Briefly, cDNA was fragmented using Bioruptor (Diagenode, Inc., Denville,N.J. USA). Fragmented cDNAs were tested for size distribution andconcentration using an Agilent Bioanalyzer 2100 or Tapestation 2200 andNanodrop.

DNA Library Construction

For each the 9 soybean samples, Illumina libraries were made fromqualified fragmented cDNA using Beckman Coulter SPRlworks HT Reagent Kit(Beckman Coulter, Inc. Indianapolis, Ind. USA, catalog #B06938) on theBiomek FXp liquid handler.

Beckman Biomek FXp (Biomek 6000, Beckman Coulter) fully automaticworkstation and a Beckman HT library kit were used to generate fragmentlibraries. The instructions were strictly followed to perform libraryconstruction. Briefly, after fragmentation the ends were repaired and‘A’ bases were added to the 3′ end of the fragments. Adapters were thenligated to both ends. The adaptor-ligated templates were furtherpurified using Agencourt AMPure SPRI beads. The adaptor-ligated librarywas amplified by ligation-mediated PCR which consisted of 10 cycles ofamplification, and the PCR product was purified using Agencourt AMPureSPRI beads again. After the library construction procedure wascompleted, QC was performed using a Nanodrop and Agilent Bioanalyzer toensure the library quality and quantity.

RNA Sequencing

Sequencing was performed on an Illumina HiSeq 2500, using Rapid run v2.0chemistry which generated paired-end reads of 106 nucleotides (nt.)according to Illumina manufacturer's instructions. The initial dataanalysis was started directly on the HiSeq 2500 System during the run.The HiSeq Control Software 2.2.58 in combination with RTA 1.18.64 (realtime analysis) performed the initial image analysis and base calling. Inaddition, bcl2fastq1.8.4 generated and reported run statistics. Data wasanalyzed using FASTQC (Babraham Institute, Cambridge, UK) comprising thesequence information which was used for all subsequent bioinformaticsanalyses. Sequences were de-multiplexed according to the 6 bp index codewith 1 mismatch allowed.

Analysis

Differential analysis of the soy transcriptome in the presence ofneutral vs beneficial fungi was performed using standard RNA-seqanalysis methods. Briefly, mapped reads overlapping with exon featureswere counted and aggregated by gene. These gene-level counts wereanalyzed with the DESeq2 R package, available through the Bioconductorsoftware repository. All possible comparisons of the three groups(control, neutral, beneficial) were performed, and the false discoveryrate method was used to adjust p-values for multiple testing. High- andlow-confidence differential gene lists were created using falsediscovery rate thresholds of 0.1 and 0.05, and log 2 fold-changethresholds of 1 and 2, respectively. Set differences were extracted,e.g., genes differentially expressed in beneficial vs control but not inneutral vs control. Gene Ontology (GO) enrichment analysis was performedfor all differential gene lists.

TABLE 500 This table shows the genes that are up-regulaled (negative logFC) or down-regulated (positive log FC) in soybean as a result oftreatment with a beneficial endophyte, as compared to formulationcontrol. Adj. Median Exp. Median Exp. SEQ ID Gene Annotation log FCp-value Beneficial Formulation 4127 GLYMA01G31730 GO: 0006952, GO,defense response −1.369956983 3.89E−08 12.63236736 3.673553109 4128GLYMA01G31921 NA −1.238022219 1.45E−06 8.528180493 2.738466863 4129GLYMA01G38630 GO: 0055114, GO, oxidation-reduction −1.0993231890.000263359 4.903703783 1.347924708 process 4130 GLYMA01G41070 GO:0008150, GO, biological_process −1.568722399 1.04E−14 13.253419793.395530442 4131 GLYMA01G43420 GO: 0006355, GO, regulation of−1.253171009 1.81E−09 22.27987154 8.177409896 transcription,DNA-dependent 4132 GLYMA01G44660 GO: 0008150, GO, biological_process−1.163160876 1.25E−05 7.245224059 1.797232944 4133 GLYMA02G01400 GO:0008152, GO, metabolic process −1.1051522 1.17E−05 5.9851850922.156679533 4134 GLYMA02G03420 GO: 0019761, GO, glucosinolate−1.015176361 4.96E−05 24.06891956 9.008550154 biosynthetic process 4135GLYMA02G04000 GO: 0080167, GO, response to karrikin −1.0703494018.30E−10 27.49585031 12.58063061 4136 GLYMA02G06150 GO: 0008150, GO,biological_process −1.034377122 2.01E−05 49.3568446 19.85942403 4137GLYMA02G09750 GO: 0006468, GO, protein phosphorylation −1.1095018921.06E−05 18.65539483 5.75161279 4138 GLYMA02G14260 GO: 0008150, GO,biological_process −1.251479824 4.10E−10 30.38164301 12.49076896 4139GLYMA02G36700 GO: 0006457, GO, protein folding 1.234514786 1.70E−085.983985525 17.25483837 4140 GLYMA02G40990 GO: 0010200, GO, response tochitin −1.627009953 7.37E−22 34.59243212 10.33408943 4141 GLYMA02G42251NA −1.411718736 9.82E−18 83.37686498 28.48614217 4142 GLYMA02G45420 GO:0006508, GO, proteolysis −1.424759326 7.78E−14 51.01901733 15.276480034143 GLYMA03G00540 GO: 0006468, GO, protein phosphorylation −1.3493914582.98E−07 9.405290859 1.803380617 4144 GLYMA03G01820 GO: 0008150, GO,biological_process −1.012023704 0.000952197 3.464573325 0.988478119 4145GLYMA03G01835 NA −1.259097901 1.11E−08 22.70628056 8.626718132 4146GLYMA03G01840 GO: 0008150, GO, biological_process −1.407747152 6.51E−1550.47616829 19.58983909 4147 GLYMA03G03480 GO: 0009733, GO, response toauxin −1.008891294 3.93E−06 14.00695871 5.543723171 stimulus 4148GLYMA03G05220 GO: 0006355, GO, regulation of −1.368776464 5.33E−0811.67294705 3.873928733 transcription, DNA-dependent 4149 GLYMA03G30410GO: 0006499, GO, N-terminal protein −1.076960853 0.000354785 4.2301308171.068669995 myristoylation 4150 GLYMA03G34780 GO: 0006979, GO, responseto oxidative 1.536202396 9.85E−09 0.576235643 3.953912477 stress 4151GLYMA03G35950 GO: 0005575, GO, cellular_component −1.037941628 6.65E−055.718030613 2.27092374 4152 GLYMA03G35980 GO: 0010150, GO, leafsenescence −1.093799446 2.45E−08 27.18357532 9.618029959 4153GLYMA03G36330 GO: 0009870, GO, defense response −1.456183569 7.05E−1414.35544394 3.606761235 signaling pathway, resistance gene- dependent4154 GLYMA03G42390 GO: 0008270, GO, zine ion binding −1.1554898677.37E−09 20.94734334 7.6919159 4155 GLYMA04G00490 GO: 0008150, GO,biological_process −1.066752001 0.000134501 5.490016192 2.066817886 4156GLYMA04G00890 GO: 0009409, GO, response to cold −1.23197541 1.83E−052.97009185 0.667918747 4157 GLYMA04G02280 GO: 0008150, GO,biological_process −1.129891407 1.65E−07 27.07697307 12.08932932 4158GLYMA04G04760 GO: 0006979, GO, response to oxidative −1.1450876391.78E−13 110.3884138 47.53681137 stress 4159 GLYMA04G09110 GO: 0006108,GO, malate metabolic −1.023288707 6.87E−08 62.46892211 27.71861586process 4160 GLYMA04G09770 GO: 0006810, GO, transport −1.0677429269.20E−06 7.225108449 2.785711064 4161 GLYMA04G11140 GO: 0006810, GO,transport −1.034043016 0.000731927 3.411272197 0.667918747 4162GLYMA04G12600 GO: 0003824, GO, catalytic activity −1.311303393 8.14E−1040.34895396 12.12689444 4163 GLYMA04G12610 GO: 0003824, GO, catalyticactivity −1.283734962 9.78E−06 1.652334971 0 4164 GLYMA04G17650 GO:0010193, GO, response to ozone −1.384727165 3.29E−11 12.870398023.594465888 4165 GLYMA04G37530 GO: 0008150, GO, biological_process1.196382319 7.27E−06 2.216290935 8.800660535 4166 GLYMA04G40700 NA−1.056299293 8.46E−11 67.64119934 32.350193 4167 GLYMA04G40710 GO:0008150, GO, biological_process −1.564590555 2.15E−18 24.556503567.278793424 4168 GLYMA04G40861 NA −1.006211746 7.60E−06 19.614815137.146730595 4169 GLYMA04G41701 NA −1.201080148 1.28E−05 5.1702094241.247337714 4170 GLYMA05G03243 NA −1.226133282 7.41E−08 14.535449515.476933727 4171 GLYMA05G22760 PF05678, PFAM, VQ motif −1.0581335730.000138289 7.995169212 2.217489269 4172 GLYMA05G25920 GO: 0008150, GO,biological_process −1.461542925 7.05E−14 22.86618395 7.368655071 4173GLYMA05G33340 GO: 0008150, GO, biological_process 1.371586716 5.70E−092.475076542 8.038398599 4174 GLYMA05G34760 GO: 0010112, GO, regulationof systemic −1.093610202 3.89E−08 18.28228693 8.348984339 acquiredresistance 4175 GLYMA05G37690 GO: 0006813, GO, potassium ion transport−1.152485783 4.56E−13 64.84867276 29.1151737 4176 GLYMA06G02340 GO:0008150, GO, biological_process −1.000797368 1.73E−07 50.9025773223.63361322 4177 GLYMA06G10450 GO: 0008150, GO, biological_process−1.442423906 2.55E−11 10.54954485 2.771861586 4178 GLYMA06G10580 GO:0008150, GO, biological_process −1.333680454 9.34E−11 13.652352163.774189183 4179 GLYMA06G13090 GO: 0006355, GO, regulation of−1.099137285 0.000134501 7.195652291 2.938842487 transcription,DNA-dependent 4180 GLYMA06G14090 GO: 0008150, GO, biological_process−1.147251562 5.98E−13 143.6465402 58.94924057 4181 GLYMA06G45020 NA−1.262217964 3.80E−15 53.83413936 18.7100657 4182 GLYMA06G45043 NA1.138574305 3.09E−10 3928.774615 8118.418788 4183 GLYMA07G06320 GO:0006355, GO, regulation of −1.006619206 2.17E−07 33.46599312 13.89270994transcription, DNA-dependent 4184 GLYMA07G11960 GO: 0010200, GO,response to chitin −1.161974193 8.23E−07 43.02133043 12.67049226 4185GLYMA07G15800 GO: 0008150, GO, biological_process 1.009903371 2.03E−065127.965314 11633.54157 4186 GLYMA07G29730 GO: 0006499, GO, N-terminalprotein −1.193477886 7.29E−05 2.437920029 0.400751248 myristoylation4187 GLYMA08G01900 GO: 0006813, GO, potassium ion transport −1.2031542732.80E−12 62.30901873 28.12669558 4188 GLYMA08G02580 GO: 0006355, GO,regulation of −1.102088699 1.08E−07 59.11095104 27.85221176transcription, DNA-dependent 4189 GLYMA08G08360 GO: 0006952, GO, defenseresponse −1.107144375 4.96E−05 6.556038754 1.870172492 4190GLYMA08G10435 NA 1.27926219 6.52E−06 1.305040358 4.642868156 4191GLYMA08G11260 GO: 0008150, GO, biological_process −1.031833196 3.58E−0951.55092715 23.63361322 4192 GLYMA08G16810 GO: 0009061, GO, anaerobicrespiration −1.153355774 1.13E−09 32.75678002 14.02629369 4193GLYMA08G17140 GO: 0007275, GO, multicellular organismal 1.0133780530.001635642 0.479710153 1.803380617 development 4194 GLYMA08G22630 GO:0009408, GO, response to heat 1.167051089 1.64E−05 1.9503360236.144852474 4195 GLYMA09G00720 GO: 0008150, GO, biological_process−1.297617667 9.76E−07 6.023027473 1.335837494 4196 GLYMA09G06840 NA1.043842712 0.000230515 1.980061233 6.236688568 4197 GLYMA09G12440 GO:0008168, GO, methyltransferase activity −1.110391457 0.0001382894.637198143 0.868294371 4198 GLYMA09G21040 NA −1.129686949 0.0001917183.015093242 0.449308236 4199 GLYMA09G30250 GO: 0010200, GO, response tochitin −1.480411528 3.22E−16 37.95040319 10.04799825 4200 GLYMA09G38930GO: 0009611, GO, response to wounding −1.114614822 3.43E−05 5.8098229612.00959965 4201 GLYMA09G41670 GO: 0006355, GO, regulation of−1.282700181 1.93E−09 17.21626437 5.127943934 transcription,DNA-dependent 4202 GLYMA10G04210 GO: 0006355, GO, regulation of−1.021042996 1.99E−05 9.380998542 4.672805655 transcription,DNA-dependent 4203 GLYMA10G22100 GO: 0055114, GO, oxidation-reduction−1.184360983 7.75E−05 1.595729473 0.179723294 process 4204 GLYMA10G37920GO: 0004497, GO, monooxygenase activity −1.440645295 3.88E−1013.27198089 3.339593736 4205 GLYMA10G39971 NA −1.199223405 2.01E−055.223510552 1.87100657 4206 GLYMA10G44160 GO: 0006355, GO, regulation of−1.469325378 1.70E−11 28.40950127 8.549359964 transcription,DNA-dependent 4207 GLYMA11G06660 GO: 0055114, GO, oxidation-reduction−1.013056688 6.65E−05 40.40225509 14.96137994 process 4208 GLYMA11G13290NA −1.186249968 1.08E−06 34.87607854 13.47924708 4209 GLYMA11G13800 GO:0005975, GO, carbohydrate metabolic −1.212845405 8.71E−11 32.3537847512.62366432 process 4210 GLYMA11G13810 GO: 0005975, GO, carbohydratemetabolic −1.025842415 0.000230184 5.330112808 2.204131866 process 4211GLYMA11G16120 NA −1.343091922 6.61E−11 16.52334971 4.313359066 4212GLYMA11G21250 GO: 0006468, GO, protein phosphorylation −1.068097020.000495067 2.77165866 0.718893178 4213 GLYMA11G25670 GO: 0010193, GO,response to ozone −1.137836997 1.03E−05 8.634782749 2.695849416 4214GLYMA11G33450 GO: 0010200, GO, response to chitin −1.387745046 4.11E−1957.82678829 19.16926804 4215 GLYMA12G00460 GO: 0006468, GO, proteinphosphorylation −1.042089407 1.75E−09 35.01739678 15.63592661 4216GLYMA12G00780 GO: 0005975, GO, carbohydrate metabolic 1.0751380280.000616457 0.443258187 1.536213118 process 4217 GLYMA12G01420 GO:0006952, GO, defense response −1.02645451 1.87E−07 30.3631858114.73731014 4218 GLYMA12G05770 GO: 0005975, GO, carbohydrate metabolic1.235797291 3.38E−07 9.663028477 25.91524739 process 4219 GLYMA12G05800GO: 0005975, GO, carbohydrate metabolic −1.014997151 7.90E−0629.83592268 13.15799932 process 4220 GLYMA12G08020 GO: 0006887, GO,exocytosis −1.088877462 8.78E−06 7.18078263 2.494675427 4221GLYMA12G09830 GO: 0000289, GO, nuclear-transcribed −1.038592224 5.61E−09269.4683333 120.4146073 mRNA poly(A) tail shortening 4222 GLYMA12G12260NA −1.305617284 9.36E−18 48.29082204 15.69609056 4223 GLYMA12G15620 GO:0005975, GO, carbohydrate metabolic −1.21921729 2.12E−08 28.8359102910.41953246 process 4224 GLYMA12G36310 GO: 0006814, GO, sodium iontransport −1.417198792 1.03E−07 6.076328601 1.335837494 4225GLYMA13G09690 GO: 0006071, GO, glycerol metabolic −1.091584652 1.88E−0729.58212608 11.0874512 process 4226 GLYMA13G09840 GO: 0006071, GO,glycerol metabolic −1.048336234 2.07E−07 45.73236789 20.63868929 process4227 GLYMA13G10010 GO: 0006468, GO, protein phosphorylation −1.182043352.97E−06 7.515459059 2.286785808 4228 GLYMA13G19560 GO: 0006355, GO,regulation of −1.2382138 5.37E−07 6.870501899 2.078896189 transcription,DNA-dependent 4229 GLYMA13G22540 NA −1.055564007 1.97E−08 31.6608700813.47924708 4230 GLYMA13G35320 GO: 0006952, GO, defense response1.440915562 2.97E−12 52.07520214 149.0804727 4231 GLYMA13G35710 GO:0008150, GO, biological_process 1.011655056 0.000625306 0.0450013921.61750965 4232 GLYMA14G05710 PTHR10499: SF51, Panther, VON −1.0798217640.000308777 1.935059842 0.138593079 WILLEBRAND FACTOR A3 4233GLYMA14G06640 GO: 0006979, GO, response to oxidative −1.2157719871.16E−08 20.25689915 6.791060885 stress 4234 GLYMA14G06900 GO: 0009408,GO, response to heat 1.019854223 0.00021457 3.195098808 9.684821834 4235GLYMA14G09571 NA −1.007062495 0.001249681 2.925090458 0.868294371 4236GLYMA14G32430 GO: 0009414, GO, response to water 1.002316095 1.01E−0610.62032843 22.59067192 deprivation 4237 GLYMA14G39300 GO: 0010200, GO,response to chitin −1.134859314 4.96E−09 71.15700599 29.02531205 4238GLYMA14G39950 GO: 0008150, GO, biological_process −1.057047859 1.33E−0819.72141739 7.553322821 4239 GLYMA15G11140 GO: 0009651, GO, response tosalt stress −1.008285337 1.31E−05 28.83591029 14.15987744 4240GLYMA15G13510 GO: 0006979, GO, response to oxidative −1.4392098 9.46E−1119.88132077 5.543723171 stress 4241 GLYMA16G06520 GO: 0008150, GO,biological_process −1.436684015 1.57E−08 5.625173959 0.988478119 4242GLYMA16G31401 NA −1.106530815 1.52E−05 9.270286684 3.118344284 4243GLYMA17G01530 GO: 0008150, GO, biological_process −1.0376148780.001129298 1.773032748 0.400751248 4244 GLYMA17G03340 GO: 0006952, GO,defense response −1.220260866 1.01E−10 372.1615091 135.9882569 4245GLYMA17G05240 GO: 0006355, GO, regulation of −1.407526282 2.79E−1317.00305986 5.8108931 transcription, DNA-dependent 4246 GLYMA17G11340GO: 0008150, GO, biological_process −1.27822077 1.25E−09 20.035270057.368655071 4247 GLYMA17G11490 GO: 0008150, GO, biological_process−1.298456505 3.81E−06 3.411272197 0.623668857 4248 GLYMA17G35430 GO:0006979, GO, response to oxidative −1.083557924 1.71E−10 130.774044253.1082335 stress 4249 GLYMA18G03066 NA −1.022521386 2.16E−0884.85539591 34.95618076 4250 GLYMA18G04770 GO: 0010200, GO, response tochitin −1.328972157 1.26E−22 78.45926054 28.58692238 4251 GLYMA18G20470GO: 0010193, GO, response to ozone −1.03304461 0.000267522 6.8758455222.137339991 4252 GLYMA18G28830 GO: 0015995, GO, chlorophyll biosynthetic−1.360956021 6.62E−07 4.850402655 1.001878121 process 4253 GLYMA18G44030GO: 0006355, GO, regulation of −1.121912469 5.61E−06 14.604509095.682316251 transcription, DNA-dependent 4254 GLYMA18G49158 NA−1.354034842 4.58E−07 4.635143342 0.801502497 4255 GLYMA18G50691 NA−1.039325485 9.07E−05 6.715942138 2.40450749 4256 GLYMA18G53250 GO:0008150, GO, biological_process 1.250925416 2.68E−08 2.8782609169.255749663 4257 GLYMA19G01440 GO: 0009408, GO, response to heat1.091071017 3.48E−13 33.43603401 78.48045279 4258 GLYMA19G34490 NA−1.064397801 0.000164104 5.265162825 1.536213118 4259 GLYMA19G35740 GO:0006355, GO, regulation of −1.062085765 4.69E−05 7.225108449 2.516126122transcription, DNA-dependent 4260 GLYMA19G37161 NA −1.1059700110.000101771 3.89098235 1.078339767 4261 GLYMA19G38570 GO: 0010150, GO,leaf senescence −1.11397824 4.23E−09 34.91223889 14.4677252 4262GLYMA19G38590 GO: 0010150, GO, leaf senescence −1.295108361 8.98E−075.540727338 1.707371297 4263 GLYMA19G41410 GO: 0005975, GO, carbohydratemetabolic 1.336821707 2.59E−06 0.132977456 2.003756241 process 4264GLYMA20G01170 GO: 0006499, GO, N-terminal protein −1.124709392 4.41E−066.715942138 2.156679533 myristoylation 4265 GLYMA20G03850 NA−1.027846502 0.000691549 4.05012525 1.247337714 4266 GLYMA20G25990 GO:0006499, GO, N-terminal protein −1.110406177 1.18E−09 60.2118620526.50918593 myristoylation 4267 GLYMA20G26600 GO: 0006952, GO, defenseresponse −1.008944076 7.29E−07 46.74508933 17.03192805 4268GLYMA20G27020 GO: 0008150, GO, biological_process −1.092005979 2.85E−1042.46413432 18.10059805 4269 GLYMA20G35180 GO: 0006355, GO, regulationof −1.034170042 9.83E−09 21.94128026 9.751613708 transcription,DNA-dependent 4270 GLYMA03G37400 GO: 0042545, GO, cell wall modification1.646163821 2.88E−09 0.213204512 2.426264 4271 GLYMA03G38840 GO:0005975, GO, carbohydrate metabolic 2.018195916 1.64E−15 0.5762356435.391699 process 4272 GLYMA07G15380 GO: 0009693, GO, ethylenebiosynthetic 1.14033694 9.07E−05 0.900027833 4.133636 process 4273GLYMA08G46450 GO: 0005975, GO, carbohydrate metabolic 2.0284939597.27E−15 0.310280731 3.684328 process 4274 GLYMA09G35840 GO: 0005975,GO, carbohydrate metabolic 3.395302467 6.40E−68 1.152471286 24.89168process 4275 GLYMA10G30340 GO: 0008150, GO, biological_process−2.087505841 1.42E−27 35.23204566 5.032252 4276 GLYMA11G02350 GO:0005975, GO, carbohydrate metabolic 2.628824882 2.44E−30 1.01272143413.47925 process 4277 GLYMA12G01510 GO: 0005975, GO, carbohydratemetabolic 3.161170918 8.63E−48 0.5400167 13.1198 process 4278GLYMA13G30440 GO: 0008150, GO, biological_process −2.347970113 7.37E−227.195652291 0.467543 4279 GLYMA15G07700 PF00264, PFAM, Common centraldomain 0.824086029 0.018602054 3.102807309 19.05067 of tyrosinase 4281GLYMA17G08400 GO: 0006032, GO, chitin catabolic process −2.0542913871.57E−22 16.26757546 2.066818 4283 GLYMA17G14890 GO: 0006869, GO, lipidtransport 1.278386816 1.57E−08 25.8419523 62.159 4284 GLYMA18G47390 GO:0009611, GO, response to wounding −2.306445262 6.24E−19 3.9006720460.089862 4285 GLYMA18G53440 GO: 0008150, GO, biological_process0.105360923 0.992007499 16.84315647 19.54162 The genes described in thistable show significant (fdr adjusted p-value <= 0.05) differences inexpression in soybean seedlings treated with a Acremonium zea sp. withbeneficial effects on soybean growth and soybean seedlings treated witha formulation (“Beneficial v Formulation”). “Median Exp. Beneficial” and“Median Exp. Formulation” represent the median expression value in cpmacross biological replicates of soy seedlings treated with thebeneficial Acremonium and formulation, respectively. “Log FC” representsthe estimate of the log2-fold-change of the contrast. “Adj. p-value”represents the false discovery rate (Benjamini & Hochberg, 1995)adjusted p-values.

TABLE 501 This table shows the genes that are up-regulated (positive logFC) or down-regulated (negative log FC) in soybean as a result oftreatment with a beneficial endophyte, as compared to a soybean treatedwith a reference microorganism. Adj. Median Exp. Median Exp. SEQ ID GeneAnnotation log FC p-value Neutral Beneficial 4162 GLYMA04G12600 GO:0003824, GO, catalytic activity 1.206357 9.85E−08 13.26698 40.34895 4201GLYMA09G41670 GO: 0006355, GO, regulation of transcription, 1.2218641.58E−06 5.909453 17.21626 DNA-dependent 4153 GLYMA03G36330 GO: 0009870,GO, defense response signaling 0.856536 0.000672 6.648135 14.35544pathway, resistance gene-dependent 4253 GLYMA18G44030 GO: 0006355, GO,regulation of transcription, 0.998764 0.001135 5.793248 14.60451DNA-dependent 4181 GLYMA06G45020 NA 0.657628 0.003708 31.22163 53.834144195 GLYMA09G00720 GO: 0008150, GO, biological_process 0.90306 0.0037082.788204 6.023027 4206 GLYMA10G44160 GO: 0006355, GO, regulation oftranscription, 0.819527 0.009033 13.67119 28.4095 DNA-dependent 4269GLYMA20G35180 GO: 0006355, GO, regulation of transcription, 0.6632670.009033 13.62622 21.94128 DNA-dependent 4167 GLYMA04G40710 GO: 0008150,GO, biological_process 0.829353 0.010992 12.55759 24.5565 4140GLYMA02G40990 GO: 0010200, GO, response to chitin 0.795223 0.0150517.04244 34.59243 4183 GLYMA07G06320 GO: 0006355, GO, regulation oftranscription, 0.748416 0.015784 18.20323 33.46599 DNA-dependent 4142GLYMA02G45420 GO: 0006508, GO, proteolysis 0.894101 0.016107 21.7383551.01902 4199 GLYMA09G30250 GO: 0010200, GO, response to chitin 0.8193310.017054 15.30126 37.9504 4250 GLYMA18G04770 GO: 0010200, GO, responseto chitin 0.787911 0.019874 39.88881 78.45926 4213 GLYMA11G25670 GO:0010193, GO, response to ozone 0.897841 0.02031 3.00749 8.634783 4150GLYMA03G34780 GO: 0006979, GO, response to oxidative −0.91553 0.0221562.078494 0.576236 stress 4222 GLYMA12G12260 NA 0.730565 0.02231 26.2759648.29082 4184 GLYMA07G11960 GO: 0010200, GO, response to chitin 0.8813150.026957 16.19823 43.02133 4131 GLYMA01G43420 GO: 0006355, GO,regulation of transcription, 0.792195 0.0384 11.50233 22.27987DNA-dependent 4223 GLYMA12G15620 GO: 0005975, GO, carbohydrate metabolic0.802313 0.040823 13.75344 28.83591 process 4270 GLYMA03G37400 GO:0042545, GO, cell wall modification 0.166032 NA 0.052762975 0.2132045124271 GLYMA03G38840 GO: 0005975, GO, carbohydrate metabolic −0.917140.022324 1.793941164 0.576235643 process 4272 GLYMA07G15380 GO: 0009693,GO, ethylene biosynthetic 0.727432 0.132533 0.265339603 0.900027833process 4273 GLYMA08G46450 GO: 0005975, GO, carbohydrate metabolic−0.44339 0.684951 0.844207607 0.310280731 process 4274 GLYMA09G35840 GO:0005975, GO, carbohydrate metabolic −1.28626 1.70E−05 4.0473928111.152471286 process 4275 GLYMA10G30340 GO: 0008150, GO,biological_process 0.531076 0.317217 17.04402084 35.23204566 4276GLYMA11G02350 GO: 0005975, GO, carbohydrate metabolic −0.39592 0.8267061.636260886 1.012721434 process 4277 GLYMA12G01510 GO: 0005975, GO,carbohydrate metabolic −0.84175 0.059336 1.503591084 0.5400167 process4278 GLYMA13G30440 GO: 0008150, GO, biological_process 0.559495 0.4726332.564949496 7.195652291 4279 GLYMA15G07700 PF00264, PFAM, Common centraldomain 0.458456 0.694846 1.618957124 3.102807309 of tyrosinase 4280GLYMA15G12600 GO: 0006869, GO, lipid transport 0.833553 0.0643823.165778525 12.27825178 4281 GLYMA17G08400 GO: 0006032, GO, chitincatabolic process 0.945666 0.000294 6.191257405 16.26757546 4282GLYMA17G14860 GO: 0006869, GO, lipid transport 0.776484 0.1052145.711320967 15.77999146 4283 GLYMA17G14890 GO: 0006869, GO, lipidtransport 0.617561 0.305278 10.76364699 25.8419523 4284 GLYMA18G47390GO: 0009611, GO, response to wounding 1.018065 0.000747 1.6189571243.900672046 4285 GLYMA18G53440 GO: 0008150, GO, biological_process−2.04965 6.81E−35 91.12165855 16.84315647 This table describes soybeangenes differentially expressed in soybean seedlings treated with anAcremonium zea sp. with neutral effects on soybean growth and soybeanseedlings treated with an Acremonium zea sp. with beneficial effects onsoybean growth. “Median Exp. Neutral” and “Median Exp. Beneficial”represent the median expression value in cpm across biologicalreplicates of soy seedlings treated with the neutral Acremonium andbeneficial Acremonium, respectively. “Log FC” represents the estimate ofthe log2-fold-change of the contrast. “Adj. p-value” represents thefalse discovery rate (Benjamini & Hochberg, 1995) adjusted p-values.

TABLE 502 This table describes gene ontology terms which aresignificantly enriched or depleted in the set of genes differentlyexpressed between soybean seedlings treated with an Acremonium zea sp.with neutral effects on soybean growth and soybean seedlings treatedwith a Acremonium zea sp. with beneficial effects on soybean growth.“Genome count” represents the number of genes associated with the GOterm that were found in the soybean genome. “Observed DEG count”represents the number of genes associated with the GO term that weredifferentially expressed in the Neutral v Beneficial contrast. “ExpectedDEG count” represents the number of genes associated with the GO termthat are expected to be found by chance in a random set selection ofthat number of genes. “Status” represents whether genes with the GO termare over or under-represented in the set of DEGs. “Adj. p-value”represents the false discovery rate (Benjamini & Hochberg, 1995)adjusted p-values. GO ID GO Description Gene ID SEQ ID GO:0000014single-stranded GLYMA15G07430, GLYMA15G07430 4286; 4286 DNA specificendodeoxyribonuclease activity GO:0003700 sequence-specificGLYMA03G34730, GLYMA03G41750, 4288; 4295; 4292; DNA bindingGLYMA05G32040, GLYMA06G11700, 4296; 4297; 4201; transcription factorGLYMA08G16190, GLYMA09G41670, 4298; 4299; 4300; activity GLYMA13G21350,GLYMA19G37410, 4301; 4302; 4303; GLYMA19G40650, GLYMA0041S00350, 4304;4305; 4288; GLYMA01G41520, GLYMA01G44230, 4306; 4292; 4307;GLYMA02G00290, GLYMA03G33070, 4308; 4297; 4309; GLYMA03G34730,GLYMA04G35380, 4310; 4298; 4311; GLYMA05G32040, GLYMA06G20400, 4312;4313; 4314; GLYMA08G14320, GLYMA08G16190, 4299; 4131; 4148;GLYMA08G18470, GLYMA13G18400, 4305; 4158; 4174; GLYMA13G21350,GLYMA15G00570, 4315; 4316; 4179; GLYMA17G06610, GLYMA18G43580, 4183;4188; 4308; GLYMA19G34740, GLYMA19G37410, 4193; 4317; 4201;GLYMA01G43420, GLYMA03G05220, 4318; 4202; 4206; GLYMA03G33070,GLYMA04G04760, 4319; 4310; 4228; GLYMA05G34760, GLYMA05G36970, 4311;4320; 4245; GLYMA06G04840, GLYMA06G13090, 4248; 4253; 4259;GLYMA07G06320, GLYMA08G02580, 4321; 4269 GLYMA08G14320, GLYMA08G17140,GLYMA09G08330, GLYMA09G41670, GLYMA10G04190, GLYMA10G04210,GLYMA10G44160, GLYMA13G17250, GLYMA13G18400, GLYMA13G19560,GLYMA15G00570, GLYMA15G19910, GLYMA17G05240, GLYMA17G35430,GLYMA18G44030, GLYMA19G35740, GLYMA19G35770, GLYMA20G35180 GO:0003950NAD+ ADP− GLYMA04G35560 4289 ribosyltransferase activity GO:0004222metalloendopeptidase GLYMA01G41750, GLYMA01G04350 4290; 4287 activityGO:0006308 DNA catabolic GLYMA15G07430, GLYMA01G20900, 4286; 4322; 4286;process GLYMA15G07430, GLYMA01G20900 4322 GO:0006879 cellular ironGLYMA13G27300, GLYMA13G27300 4291; 4291 ion homeostasis GO:0006970response to GLYMA05G32040, GLYMA09G41670, 4292; 4201; 4292; osmoticstress GLYMA05G32040, GLYMA03G05220, 4148; 4201; 4253 GLYMA09G41670,GLYMA18G44030 GO:0008237 metallopeptidase GLYMA01G41750, GLYMA01G043504290; 4287 activity GO:0008270 zinc ion binding GLYMA01G41750,GLYMA01G04350, 4290; 4287; 4305; GLYMA03G33070, GLYMA09G26100, 4335;4305; 4154; GLYMA03G33070, GLYMA03G42390, 4158; 4159; 4316;GLYMA04G04760, GLYMA04G09110, 4206; 4228; 4248; GLYMA06G04840,GLYMA10G44160, 4259; 4321 GLYMA13G19560, GLYMA17G35430, GLYMA19G35740,GLYMA19G35770 GO:0009611 response to GLYMA06G45240, GLYMA06G45280, 4293;4323; 4324; wounding GLYMA06G45370, GLYMA06G45410, 4325; 4326; 4327;GLYMA12G32750, GLYMA13G37720, 4328; 4284; 4329; GLYMA13G37770,GLYMA18G47390, 4293; 4324; 4325; GLYMA01G41290, GLYMA06G45240, 4326;4330; 4331; GLYMA06G45370, GLYMA06G45410, 4332; 4327; 4333;GLYMA12G32750, GLYMA13G23680, 4328; 4311; 4334; GLYMA13G35820,GLYMA13G35850, 4284; 4158; 4316; GLYMA13G37720, GLYMA13G37750, 4200;4221; 4311; GLYMA13G37770, GLYMA15G00570, 4248; 4284 GLYMA18G06810,GLYMA18G47390, GLYMA04G04760, GLYMA06G04840, GLYMA09G38930,GLYMA12G09830, GLYMA15G00570, GLYMA17G35430, GLYMA18G47390 GO:0010120camalexin GLYMA03G05220, GLYMA09G41670, 4148; 4201; 4253 biosyntheticprocess GLYMA18G44030 GO:0016891 endoribonuclease GLYMA15G07430,GLYMA15G07430 4286; 4286 activity, producing 5′-phosphomonoestersGO:0034605 cellular response GLYMA03G05220, GLYMA09G41670, 4148; 4201;4253 to heat GLYMA18G44030 GO:0043765 T/G mismatch-specificGLYMA15G07430, GLYMA15G07430 4286; 4286 endonuclease activity GO:0046592polyamine oxidase GLYMA10G11700, GLYMA10G11700 4294; 4294 activityGO:0050660 flavin adenine GLYMA04G12600, GLYMA10G11700, 4162; 4294;4294; dinucleotide binding GLYMA10G11700, GLYMA19G44870, 4336; 4162;4163; GLYMA04G12600, GLYMA04G12610, 4336 GLYMA19G44870 GO:0070370cellular heat GLYMA03G05220, GLYMA09G41670, 4148; 4201; 4253 acclimationGLYMA18G44030 GO:0071369 cellular response GLYMA13G27300, GLYMA13G273004291; 4291 to ethylene stimulus GO:0071732 cellular responseGLYMA13G27300, GLYMA13G27300 4291; 4291 to nitric oxide GO:0072593reactive oxygen GLYMA04G35560 4289 species metabolic process

Genes that are modulated in soybean in response to treatment with abeneficial endophyte include those involved in a variety of plantprocesses, such as plant defense (including responses to chitin andwounding), stress responses (including salt stress, water deprivation,cold, ozone, heat, osmotic), defense against oxidative stress(oxidation-reduction process, monooxygenase activity,oxidation-reduction process, ion binding, nitric oxide). For example,expression of genes involved in the following processes were modulated:cell wall modification, defense response, oxidation-reduction process,biological process, regulation of transcription, metabolic process,glucosinolate biosynthetic process, response to karrikin, proteinphosphorylation, protein folding, response to chitin, proteolysis,response to auxin stimulus, DNA-dependent regulation of transcription,N-terminal protein myristoylation, response to oxidative stress,cellular component, leaf senescence, resistance gene-dependent defenseresponse signaling pathway, zinc ion binding, response to cold, malatemetabolic process, transport, catalytic activity, response to ozone, VQmotif, regulation of systemic acquired resistance, potassium iontransport, anaerobic respiration, multicellular organismal development,response to heat, methyltransferase activity, response to wounding,oxidation-reduction process, monooxygenase activity, oxidation-reductionprocess, carbohydrate metabolic process, exocytosis, nuclear-transcribedmRNA poly(A) tail shortening, sodium ion transport, glycerol metabolicprocess, response to water deprivation, response to salt stress, andchlorophyll biosynthetic process.

Example 6: Functional Characterization of Endophytes (Microbe RNA-SEQExperiments)

This Example describes the ability of synthetic compositions comprisingplant seeds and a single endophyte strain or a plurality of endophytestrains described herein, to confer beneficial traits to a host plant.Among other things, this Example provides exemplary characterization ofmodulations in a beneficial endophyte's transcriptome in response tohost plant interactions, as compared to transcriptome changes in thetranscriptome of a neutral (e.g., non-beneficial and non-pathogenic)microbe of the same genus.

RNA sequencing was used to explore differences in mRNA expression ofgenes common to the two strains of Acremonium zeae.

Among other things, this Example describe the ability of host plants(e.g., host plants described herein, e.g., dicots, e.g., soy, peanuts,and monocots, e.g., corn, soy, wheat, cotton, sorghum) to differentiallymodulate the transcriptome of a beneficial endophyte as compared to thetranscriptome of a neutral microbe of the same genus. This Exampledescribes surprising and unexpected modulations in the transcriptome ofa beneficial endophyte in response to whole plant homogenate, comparedto a neutral fungal strain of the same genus.

In particular, this Example describes an exemplary transcriptomiccomparison between the functional capacity of a beneficial fungalendophyte genome and the genome of a neutral fungal microbe of the samegenus. Briefly, each set of microbial predicted genes was annotated withpathway and orthologous group information from the KEGG database.Pathways and ortholog groups appearing in one genome but not the otherwere extracted and manually explored for biological relevance to thephenotype differences.

Fungal Biomass

Beneficial (SYM00577) and neutral (SYM00300) fungal strains ofAcremonium zeae were initially streaked onto PD agar and incubated atroom temperature until colony formation. Distinct plugs consisting ofspores and mycelia were used to inoculate 125 mL PD broth and culturedfor 5 days at room temperature with agitation (200 RPM). Each strain wasgrown in three biological replicates in duplicates totaling 12 flasks.

On day 5 of culture, 1 mL of total plant homogenate obtained from 6 dayold soybean seedlings extracted with 50 mM Phosphate-buffered saline(PBS) at a ratio of 2 mL buffer/gram plant mass was added to the fungi.The plant homogenate solution was prepared in three replicates, and eachreplicate was applied to the corresponding beneficial and neutral fungalcultures. One mL of PBS solution was applied to each fungal biologicalreplicate as the negative control.

Fungal biomass was harvested 24 hours after the addition of either theplant homogenate or PBS only solutions by centrifuging at 4500 RPM for20 minutes in 50 mL Falcon tubes to allow culture separation prior tothe removal of supernatant. Fungal tissues were stored immediately in−80° C. until total RNA isolation using standard extraction method usingTriReagent (Sigma-Aldrich, St. Louis, Mo., USA) and purification withRNeasy Mini Kit (Qiagen, Hilden, Germany).

Fungal RNA-SEQ

Initial quality control was performed using Agilent Bioanalyzer andTapestation.

rRNA Depletion

1 μg of total RNA was subjected to rRNA depletion using the RiboZeroYeast kit (Epicentre Biotechnologies, Illumina.com, catalog #MRZY1306).Manufacturer's instructions were strictly followed to perform rRNAdepletion.

Stranded cDNA Preparation

After rRNA depletion, depletedRNA was used to generate 1-2 ug of cDNAusing: Illumina TruSeq Stranded Total RNA LT kit (Illumina.com, catalog#RS-122-2201). Manufacturer's instructions were strictly followed toperform cDNA construction; and library construction.

RNA Sequencing

Sequencing was performed on an Illumina HiSeq 2500, using Rapid run v2.0chemistry which generated paired-end reads of 106 nucleotides accordingto Illumina manufacturer's instructions. The initial data analysis wasstarted directly on the HiSeq 2500 System during the run. The HiSeqControl Software 2.2.58 in combination with RTA 1.18.64 (real timeanalysis) performed the initial image analysis and base calling. Inaddition, bcl2fastq1.8.4 generated and reported run statistics. Data wasanalyzed using FASTQC (Babraham Institute, Cambridge, UK) comprising thesequence information which was used for all subsequent bioinformaticsanalyses. Sequences were de-multiplexed according to the 6 bp index codewith 1 mismatch allowed.

Analysis

Expression levels for each gene were quantified as transcripts permillion (TPM) using Cufflinks. The Blast Best Reciprocal Hits (BRH)method was used to define orthologous groups for similar gene pairsacross species. Expression was mapped directly to BRH groups to createan expression matrix and the limma method was used to uncover genes (1)differentially expressed with vs without plant homogenate within eachspecies, (2) differentially expressed across species within each planthomogenate condition, and (3) responding differently to plant homogenatein the different species. The false discovery rate method was used toadjust p-values for multiple testing. In each case, significance wasdefined as adjusted p-value less than 0.05 and absolute log 2 foldchange greater than 2.

Functional and Comparative Genomics

Prior to applying differential expression analysis, the functionalcapabilities of a beneficial and neutral Acremonium zeae, i.e., SYM00577(beneficial) and SYM00300 (neutral), were contrasted at the genefunction (GO) and pathway level. A shared goal of both the genomecomparison and the transcriptome analyses was the construction oforthologous groups. In the case of comparative genomics, annotations ofthese orthologs provided an overview of shared capabilities, while forRNA-seq they provided anchors for comparison of expression data, i.e.rows in the expression matrix.

Differential KEGG Orthology Groups

The unique and shared orthology group (OG) terms were counted forSYM00577 and SYM00300. Most KO terms were shared by both strains, with62 terms found in SYM00300 only, and 207 terms found in SYM00577 only,with 2,676 KO terms overlapping between both strains. This process wasrepeated for KEGG Pathways, and the total and shared number of pathwayswas again similar, with 324 of the pathways shared between strains.Unique pathways in SYM00577 that were not present in SYM00300, include,but are not limited to, indole diterpene alkaloid biosynthesis,biosynthesis of 12-, 14- and 16-membered macrolides, peptidoglycanbiosynthesis, glycosphingolipid biosynthesis—lacto and neolacto series,indole alkaloid biosynthesis, type I polyketide structures, biosynthesisof siderophore group nonribosomal peptides, beta-Lactam resistance,sphingolipid signaling pathway, Vibrio cholera pathogenic cycle, centralcarbon metabolism in cancer, choline metabolism in cancer, andnicotinate and nicotinamide metabolism. Exemplary KEGG Pathwaydifferences for SYM00577 are illustrated below in Table 600.

TABLE 600 Exemplary KEGG Pathways present in SYM0577, but absent inSYM0300 Number KEGG Term KEGG Term Description of Genes ko00403 Indolediterpene alkaloid biosynthesis 1 ko00522 Biosynthesis of 12-, 14- and16- 1 memebered macrolides ko00550 Peptidoglycan biosynthesis 2 ko00601Glycosphingolipid biosynthesis - 1 lacto and neolacto series ko00901Indole alkaloid biosynthesis 1 ko01052 Type I polyketide structures 1ko01053 Biosynthesis of siderophore group 2 nonribosomal peptidesko01501 Beta-Lactam resistance 7 ko04071 Sphingolipid signaling pathway46 ko05111 Vibrio cholera pathogenic cycle 1 ko05230 Central carbonmetabolism in cancer 29 ko05231 Choline metabolism in cancer 30

In the above example, the Sphingolipid signaling pathway included 46genes. To determine whether all of the genes (i.e., orthologous groups)in the pathway were unique to only SYM00577, a query was performed todetermine which of the Sphingolipid pathway genes in SYM00577 do notshare any KEGG OG terms with SYM00300 genes.

Interestingly, even though the Sphingolipid Signaling Pathway annotationis attached to 46 genes in SYM00577 but no genes in SYM00300, only oneorthologous group from that pathway (sphingomyelin phosphodiesterase,annotating 4 genes) is not present in SYM300.

Unique pathways in SYM00300 that were not present in SYM00577, include,but are not limited to, beta-Lactam resistance, DDT degradation, Flavoneand flavonol biosynthesis, and ECM-receptor interaction. Exemplary KEGGPathway differences for SYM00300 are illustrated below in Table 700.

TABLE 601 Exemplary KEGG Pathways present in SYM0300, but absent inSYM0577 Number KEGG Term KEGG Term Description of Genes ko00312Beta-Lactam resistance 4 ko00351 DDT degradation 3 ko00944 Flavone andflavonol biosynthesis 1 ko04512 ECM-receptor interaction 2

Blast Best Reciprocal Hits (BBRH)

The NCBI Blast+software was installed and used to build blast databasesfrom each set of amino acid sequences, then each transcriptome wasblasted against the database created from the other. Best ReciprocalHits (BRH) were calculated by filtering for high percent identity,gathering the best hits, and joining the targets from one output withthe queries from the other. The result was a query-target-reciprocaltrio, which was filtered for trios where the query was the same as itsreciprocal. The e-value and bitscores from the two blast outputs wereaveraged (since they are asymmetric) for the BRH pairs, and an orthologgroup identifier was created.

Calculation of in-Paralogs

In-paralogs are paralogs that are the result of speciation first, thenduplication of the genes later. In-paralogs are more likely to retainthe same function as the ortholog than out-paralogs, which representduplication, followed by speciation. Considering the high proportion ofSYM00300 genes that have BRH orthologs, along with the realization thatSYM00577 has nearly twice as many transcripts, we considered thepossibility of a major genome duplication event somewhere in thephylogenetic history of SYM00577, and extended the orthologous groups toinclude in-paralogs.

An important step after BRH is, for each orthologous pair, to includesame-species genes more similar to each member of the pair than thecross-species ortholog similarity. This was accomplished usingall-versus-all Blast within the same species, to expand our orthologousgroups.

Another approach to building ortholog groups was to apply a threshold tothe same-species hits for each member of the ortholog pairs. To find thebest threshold, we explored the distribution of scores in theseBRH/same-species tables described above, normalizing by the orthologscore.

RNA-SEQ Cross-Species Comparison

RNA-seq cufflinks FPKM values were generated for two species of fungus(Acremonium zeae), with three biological replicates each. An expressionmatrix was built using orthologouos groups, to explore the structure ofthe data, characterize data quality, and to elucidate pathway-levelexpression differences between SYM00577 and SYM00300.

TABLE 602 Median Median SEQ ID SEQ ID Exp. Exp. SYM- SYM577 SYM- SYM300SYM- SYM- B- t- Adj. 00577 gene 00300 gene Description 00577 00300 LogFC statistic statistic p-value 694 g3058.t1 2499 g1604.t1 0 5.6259625.651891 7.35527 14.19007 8.51E−06 695 g3790.t1 2501 g2628.t1 K12486:SMAP 0 6.121031 5.983809 6.039604 11.33524 1.91E−05 681 g4581.t1 3296g4123.t1 K00574: E2.1.1.79, 0.511902 7.31261 7.115847 5.836125 10.979392.24E−05 cfa 682 g9772.t1 3297 g936.t1 K06874: K06874 1.832874 7.062985.150347 5.58339 10.56106 2.71E−05 1454 g3066.t1 2510 g11773.t1 04.229364 4.33707 5.111231 9.840967 4.33E−05 1455 g2768.t1 3298 g9143.t1K03937: NDUFS4 0 3.159447 3.192054 5.100931 9.826062 4.35E−05 1456g21086.t1 2530 g6575.t1 6.213302 0 −6.32587 4.86651 −9.49529 5.53E−051457 g13116.t1 2518 g7771.t1 0 4.229765 4.831879 4.862002 9.4890835.54E−05 1458 g900.t1 3299 g9375.t1 0 2.925165 2.991998 4.8243139.437402 5.73E−05 693 g2076.t1 2498 g2520.t1 3.957232 13.01167 9.7295194.68583 9.250787 6.67E−05 1459 g5141.t1 3300 g3839.t1 K06662: HRAD17,1.158624 7.175348 6.392146 4.57545 9.105599 7.49E−05 RAD24 1460g10898.t1 2515 g5903.t1 0 2.733166 2.603795 4.241238 8.683922 0.0001071461 g19933.t1 3301 g3124.t1 K10885: XRCC5, 0 2.454643 2.568635 4.1628038.588628 0.000116 KU80, G22P2 685 g6380.t1 2492 g764.t1 K05857: PLCD3.201415 9.359327 5.628694 3.892588 8.270189 0.000152 689 g849.t1 2496g9453.t1 K06997: K06997 2.698993 7.96329 5.067599 3.750578 8.1086280.000171 1462 g156.t1 3302 g5221.t1 0 2.981748 2.98057 3.513183 7.8468430.000215 1463 g10541.t1 3303 g6687.t1 K17862: PPOC 0 2.880335 2.9566423.496903 7.829254 0.000219 1464 g15671.t1 3304 g6482.t1 K11771: SWI1, 02.123699 2.319853 3.367017 7.690534 0.000246 ADR6 1465 g5602.t1 2531g7524.t1 K14774: UTP25, 0 4.214818 5.146089 3.215759 7.532472 0.000282DEF 1466 g4223.t1 3305 g1757.t1 2.289499 7.236816 5.448174 3.2069717.523401 0.000284 684 g2536.t1 3306 g3569.t1 9.671862 2.518007 −7.857363.098463 −7.41238 0.000316 1467 g8228.t1 3307 g10052.t1 K01674: cah5.638975 1.15932 −4.58017 2.941341 −7.25475 0.000366 1468 g10616.t1 3308g4156.t1 K15562: BUR1, 0 4.260933 4.233331 2.939239 7.252662 0.000366SGV1 1469 g10359.t1 3309 g7715.t1 2.199706 9.30437 7.40778 2.9072477.221016 0.000378 1470 g12048.t1 3310 g810.t1 0.205106 6.22836 5.6964982.79987 7.11586 0.000412 1471 g7057.t1 3311 g6310.t1 K05610: UCHL5,2.367427 6.390825 4.178102 2.772937 7.089735 0.000422 UCH37 680 g1340.t12553 g523.t1 0 5.30819 5.122003 2.739527 7.057466 0.000434 1472 g5411.t13312 g8610.t1 0 5.724304 5.482331 2.691237 7.011091 0.000454 1474g2755.t1 3314 g9155.t1 K13106: BUD13, 0 2.648734 2.611976 2.637236.959594 0.000475 CWC26 1473 g9212.t1 3313 g11325.t1 K03380: 0.6958298.890455 7.737352 2.638623 6.960917 0.000475 E1.14.13.7 1475 g7541.t13315 g7266.t1 K01230: MAN1 0.593738 3.991249 3.523245 2.589692 6.9145820.000494 1476 g10543.t1 3316 g6689.t1 K11866: STAMBP, 0 2.5128212.348519 2.557397 6.88417 0.000506 AMSH 1477 g1098.t1 3317 g4042.t1 08.363912 7.407417 2.550651 6.877834 0.000509 1478 g5757.t1 3318 g5200.t1K16261: YAT 2.629263 6.731656 4.004055 2.491406 6.822441 0.000533 1479g6616.t1 3319 g11275.t1 K00128: E1.2.1.3 14.15644 4.764987 −7.94962.391867 −6.73036 0.000579 676 g7741.t1 2557 g7091.t1 7.176506 3.981694−3.40286 2.312767 −6.65805 0.000618 1480 g3094.t1 3320 g11797.t1 K02155:0.181741 4.905207 4.139345 2.177837 6.536419 0.000699 ATPeV0C, ATP6L1481 g4793.t1 3321 g3693.t1 0.802943 6.094219 5.125954 2.035034 6.4099580.00079 1482 g4553.t1 3322 g4081.t1 1.09266 4.629 3.630404 1.9870316.367956 0.000827 1483 g2790.t1 3323 g5023.t1 2.621767 6.913986 4.3392071.945501 6.331819 0.000856 1484 g12353.t1 3324 g12077.t1 7.0445271.163008 −6.15638 1.883313 −6.27805 0.0009 1485 g9391.t1 2535 g3643.t1K12821: PRPF40, 3.337644 7.951706 4.079618 1.87347 6.269579 0.000908PRP40 1486 g501.t1 2522 g5516.t1 K11713: PGTB1 0.17786 7.158208 5.9701831.860221 6.25819 0.000918 1487 g4315.t1 3325 g1973.t1 K00507: SCD,2.439884 8.285639 5.723788 1.809797 6.215014 0.000956 desC 1488 g9843.t13326 g9771.t1 K00799: GST, gst 8.277156 1.535981 −6.40337 1.808206−6.21366 0.000956 1489 g11092.t1 3327 g7982.t1 2.025136 6.7988454.871183 1.802892 6.209122 0.000958 1490 g11703.t1 3328 g6616.t1 K01785:galM, 5.853172 0.587191 −5.06599 1.752712 −6.16645 0.001006 GALM 1491g11062.t1 3329 g1580.t1 0 8.467134 6.867295 1.691984 6.115148 0.0010641492 g13143.t1 3330 g4290.t1 K10878: SPO11 0 2.383986 2.169112 1.689326.112906 0.001065 1493 g10366.t1 2548 g5460.t1 0 4.099839 3.9727781.675269 6.101093 0.001078 1494 g9622.t1 3331 g7240.t1 K01648: ACLY 02.029549 2.402941 1.580259 6.02172 0.00118 677 g13489.t1 2556 g8733.t14.049293 1.53096 −2.39019 1.568038 −6.01157 0.001191 1495 g11681.t1 3332g10864.t1 K01081: E3.1.3.5 2.030435 5.800198 3.546964 1.557877 6.0031490.001197 1496 g13112.t1 3333 g7720.t1 0 2.5721 2.197403 1.547012 5.994150.001208 1497 g6237.t1 2500 g7135.t1 4.217621 11.98228 7.390343 1.5243735.975438 0.00123 1498 g5325.t1 2546 g2235.t1 K17794: TIM23 5.3936389.737867 4.665515 1.490748 5.947736 0.001262 1499 g7356.t1 3334 g10411.t1 5.363476 2.004245 −4.00808 1.46351 −5.92537 0.001296 1500 g502.t1 2516g5517.t1 6.13678 0.881592 −5.04567 1.401059 −5.87436 0.001355 1501g8003.t1 3335 g3392.t1 1.075006 6.028587 4.451645 1.395621 5.8699340.001362 691 g5563.t1 2493 g7478.t1 4.683265 9.926473 4.734657 1.3882095.863907 0.00137 1502 g973.t1 3336 g8044.t1 K12733: PPIL1 0 4.4466274.444962 1.37841 5.855946 0.001379 1503 g9616.t1 3337 g7246.t1 03.761644 3.227741 1.346391 5.829996 0.001416 1504 g2349.t1 3338 g9226.t1K10865: MRE11 5.092776 8.748668 3.95033 1.335801 5.821433 0.001427 1505g2683.t1 2507 g4140.t1 5.881648 1.482684 −3.92467 1.322012 −5.81030.001445 1506 g3045.t1 2533 g1615.t1 3.526626 10.01023 6.461973 1.2674615.766418 0.00152 1507 g2056.t1 3339 g2541.t1 0 2.16783 2.561107 1.2164595.725628 0.001583 521 g11059.t1 2317 g2900.t1 K01074: PPT 0 3.4179293.812645 1.160246 5.680931 0.001668 1508 g7593.t1 3340 g7644.t1 K10577:UBE2I, 5.000466 0 −4.49434 1.150461 −5.67318 0.001683 UBC9 1509 g1121.t13341 g220.t1 0.238182 9.960466 8.035072 1.140622 5.665391 0.00169 1510g13554.t1 3342 g4591.t1 0 7.155818 7.18618 1.13793 5.663262 0.0016941511 g10068.t1 3343 g4260.t1 3.254602 6.373357 2.860288 1.0966135.630659 0.001757 1512 g3061.t1 3344 g11768.t1 0 2.736145 2.4497581.082316 5.619411 0.001776 1513 g7120.t1 3345 g5585.t1 K01537: E3.6.3.86.177509 2.088352 −4.42526 1.079268 −5.61702 0.001776 1514 g1980.t1 3346g6240.t1 4.780929 1.696677 −3.47296 1.055478 −5.59834 0.001816 1515g15450.t1 3347 g6505.t1 0 3.663174 4.662175 1.041385 5.587303 0.0018371516 g10937.t1 3348 g9861.t1 3.34381 8.292693 5.149782 1.007277 5.5606520.001901 1517 g2104.t1 3349 g2481.t1 0 8.858449 6.876201 0.9474235.514113 0.00201 1518 g1101.t1 3350 g4046.t1 0 4.4026 5.770884 0.9361285.505363 0.002025 678 g2539.t1 2558 g3572.t1 2.326788 6.873537 4.8188420.882431 5.463904 0.002121 1519 g3140.t1 3351 g5042.t1 0 2.3211662.269216 0.871446 5.45545 0.002145 1520 g5369.t1 3352 g9557.t1 3.9085886.910264 3.013639 0.855938 5.443533 0.002178 1521 g12261.t1 3353g7374.t1 K00480: 0 8.154209 8.090694 0.846077 5.435964 0.002195E1.14.13.1 1522 g9519.t1 3354 g6593.t1 K03126: TAF12 0 9.766076 7.6634960.828036 5.422137 0.002231 686 g857.t1 2491 g9451.t1 K01950: E6.3.5.1,3.88692 0.53345 −3.15682 0.77121 −5.37875 0.002339 NADSYN1, QN51, nadE1523 g8434.t1 2550 g10211.t1 0 5.304746 5.464585 0.750938 5.3633280.002378 1524 g6597.t1 3355 g10126.t1 0 4.518563 5.208532 0.74287 5.35720.002397 1525 g5093.t1 3356 g2950.t1 K14688: SLC30A1, 0 2.4093932.458919 0.737239 5.352927 0.0024 ZNT1 1526 g823.t1 3357 g8190.t13.431051 7.673807 3.935357 0.734868 5.351128 0.002404 1527 g839.t1 3358g9466.t1 0 4.219241 4.683516 0.682084 5.311188 0.002522 1528 g13121.t13359 g11183.t1 0 6.54144 6.317655 0.656359 5.291798 0.002581 1529g847.t1 3360 g9458.t1 8.023071 3.66916 −3.61918 0.631424 −5.273050.002636 1530 g4627.t1 3361 g6024.t1 0.792826 6.42714 5.759738 0.6308035.272583 0.002636 1531 g10595.t1 3362 g10624.t1 K17987: NBR1 0 2.092362.123128 0.620131 5.264574 0.00266 1532 g12318.t1 3363 g7423.t1 K00166:0 2.598413 2.602354 0.593035 5.244275 0.002723 BCKDHA, bkdA1 1533g12695.t1 3364 g8902.t1 K10842: MNAT1 0 3.108472 2.951239 0.5600725.219651 0.002803 1534 g14294.t1 3365 g4038.t1 K02980: RP-S29e, 5.8829873.465017 −2.42606 0.543504 −5.2073 0.002847 RPS29 1535 g7862.t1 3366g10519.t1 K13690: CMT1 4.585103 6.930322 2.588027 0.531605 5.1984480.002873 1536 g2863.t1 3367 g11267.t1 0.167864 4.829719 5.5522880.513015 5.184633 0.002917 1537 g1455.t1 2542 g6968.t1 4.374836 10.805246.455862 0.511076 5.183194 0.00292 1538 g2438.t1 3368 g6704.t1 9.0911531.287615 −7.87656 0.465153 −5.14918 0.003038 1539 g667.t1 3369 g2708.t1K10256: FAD2 0.327373 4.952806 4.589933 0.444695 5.134069 0.003073 1540g4890.t1 3370 g4524.t1 K01530: E3.6.3.1 5.691668 0.913041 −4.255940.443497 −5.13319 0.003074 1542 g2756.t1 3372 g9154.t1 0 2.2056092.199562 0.441939 5.132036 0.003074 1541 g20204.t1 3371 g9206.t1 K00274:MAO, 0 6.517404 6.487337 0.442311 5.132311 0.003074 aofH 1543 g2398.t13373 g9298.t1 0 5.749657 5.429453 0.437917 5.12907 0.003085 1544g9984.t1 3374 g9679.t1 0 7.061175 7.03614 0.33213 5.051456 0.003396 1545g15304.t1 3375 g10452.t1 1.631174 5.484335 3.961905 0.302009 5.0294950.00348 1547 g1470.t1 3377 g6945.t1 6.211143 0.601353 −6.20846 0.295485−5.02475 0.003494 1546 g11003.t1 3376 g1982.t1 0 6.436399 5.1979880.296732 5.025654 0.003494 1548 g142.t1 3378 g5823.t1 K09051: SKO1,2.033429 6.991069 5.119512 0.271682 5.007443 0.003566 ATF1, PCR1 1549g39.t1 3379 g2832.t1 K04450: ATF2, 2.082302 6.377889 3.852174 0.213064.964987 0.003764 CREBP1 1550 g8675.t1 3380 g10949.t1 4.582792 1.158136−3.14557 0.202072 −4.95705 0.003807 1551 g1012.t1 3381 g8081.t1 K01027:OXCT 5.414227 8.052451 2.663064 0.177006 4.938984 0.003878 1552 g2399.t13382 g9299.t1 1.458025 7.000976 4.992111 0.176335 4.938501 0.003878 1553g6515.t1 3383 g2075.t1 K02950: RP-S12, 1.845883 4.922544 2.9367320.153955 4.922403 0.003952 MRPS12, rpsL 1554 g6586.t1 2539 g10115.t15.631067 0.472025 −4.60323 0.143733 −4.91506 0.003983 1555 g8523.t1 3384g6295.t1 0 7.66857 6.377663 0.128487 4.904122 0.004038 1556 g6667.t13385 g2221.t1 2.68424 6.205712 2.966025 0.118613 4.897045 0.00407 1557g12827.t1 3386 g7851.t1 0 4.848962 3.8249 0.081084 4.870203 0.0042131558 g5681.t1 3387 g2305.t1 0 5.574437 5.607999 0.076246 4.8667490.004223 1559 g8598.t1 3388 g11593.t1 3.906492 6.364882 2.4140390.063154 4.857409 0.004267 1560 g14604.t1 3389 g6507.t1 0.9874545.421424 4.548644 0.028742 4.83291 0.004395 1561 g3926.t1 2519 g3966.t15.357872 3.212704 −2.19688 −0.01172 −4.8042 0.00456 1562 g3438.t1 3390g4707.t1 1.724857 6.502863 4.96045 −0.02749 4.793029 0.004613 1563g1922.t1 3391 g6158.t1 K08334: BECN1, 0.398499 5.785388 4.960056−0.03595 4.787047 0.004637 VP530, ATG6 1564 g3435.t1 3392 g4711.t1 08.300404 6.565756 −0.04588 4.780026 0.004676 1565 g11568.t1 3393g4160.t1 K11322: EPC 2.908649 5.395163 2.502674 −0.05175 4.7758780.004698 1566 g4022.t1 3394 g3195.t1 6.571337 1.444687 −5.93348 −0.05319−4.77486 0.004702 1567 g1119.t1 3395 g218.t1 K15161: CCNC, 0 4.6982334.08668 −0.05414 4.774192 0.004703 SSN8 1568 g5372.t1 3396 g9560.t15.009004 0.930924 −4.29137 −0.05628 −4.77268 0.00471 1569 g8513.t1 3397g6303.t1 K01417: E3.4.24.- 2.66779 6.304272 3.371495 −0.06746 4.7647930.004752 1570 g10723.t1 3398 g4265.t1 K15078: SLX1 6.249677 1.09824−5.32732 −0.07338 −4.76062 0.004767 1571 g7955.t1 3399 g10265.t17.449289 0.568709 −6.91497 −0.08661 −4.7513 0.004818 1572 g8436.t1 3400g7726.t1 K08257: 0 5.100303 5.10056 −0.1098 4.73499 0.004903 E3.2.1.1011573 g1465.t1 3401 g6950.t1 4.476144 0.61942 −4.17994 −0.11145 −4.733830.004908 1574 g2407.t1 3402 g9484.t1 K13127: 7.768564 2.987939 −3.79401−0.11976 −4.728 0.00494 RNF113A, CWC24 1575 g2487.t1 3403 g3514.t1K15192: BTAF1, 3.532261 7.801782 4.747107 −0.1259 4.723684 0.00496 MOT11576 g6309.t1 3404 g3004.t1 2.982283 6.81987 3.754204 −0.13074 4.7202890.004976 1577 g1705.t1 3405 g4639.t1 1.748524 7.933591 6.241738 −0.137734.715388 0.005007 1578 g6321.t1 3406 g3017.t1 9.8442 5.01489 −4.79374−0.14476 −4.71045 0.005035 1579 g4284.t1 3407 g1936.t1 K18174: COA21.986154 6.571374 4.216021 −0.15159 4.705676 0.005055 1580 g20937.t13408 g7417.t1 K01266: dmpA 1.071718 4.362008 3.114427 −0.16727 4.6946960.005126 1581 g6962.t1 3409 g6429.t1 5.332152 0.25936 −5.40138 −0.16906−4.69345 0.005132 1582 g18713.t1 3410 g4630.t1 K03083: GSK3B 1.3336514.783178 4.745248 −0.17254 4.69101 0.005148 1583 g8296.t1 3411 g5088.t15.102827 0.74787 −5.06033 −0.17731 −4.68768 0.005171 1584 g1028.t1 3412g8097.t1 K10352: MYH 0 5.91366 5.909517 −0.18093 4.685146 0.005187 1585g7984.t1 3413 g10232.t1 4.17451 0 −3.96717 −0.18723 −4.68075 0.0052151586 g2260.t1 3414 g10672.t1 0 11.59719 8.078404 −0.20485 4.6684520.005296 1587 g2057.t1 3415 g2540.t1 0 3.495725 2.912854 −0.217614.659559 0.005358 1265 g16176.t1 2509 g5232.t1 4.464184 8.0463223.412183 −0.22053 4.657525 0.005368 1588 g710.t1 3416 g9945.t1 3.0045125.305027 3.457727 −0.26143 4.629086 0.005573 1589 g11909.t1 3417g11960.t1 K00967: PCYT2 4.581714 0.355634 −4.34247 −0.2642 −4.627160.005582 1590 g133.t1 3418 g5828.t1 0 6.458979 5.351051 −0.2661 4.6258460.005584 1591 g16811.t1 3419 g6747.t1 5.812564 0.429992 −4.86386−0.27492 −4.61972 0.005629 1592 g1007.t1 3420 g8077.t1 8.250805 2.385735−4.65062 −0.27955 −4.61651 0.005649 1593 g2691.t1 3421 g3101.t1 6.592470.374474 −6.18721 −0.28128 −4.61531 0.005656 1594 g941.t1 3422 g9318.t1K01067: E3.1.2.1, 1.499245 7.499861 6.073538 −0.318 4.5899 0.005824 ACH11595 g4067.t1 3423 g3251.t1 3.814933 6.244839 2.600899 −0.32454 4.5853830.005862 1596 g7999.t1 3424 g3379.t1 3.95884 1.293984 −3.01927 −0.36383−4.55828 0.006086 1597 g6280.t1 3425 g12254.t1 K13719: OTU1, 10.875483.850161 −7.09783 −0.38264 −4.54533 0.006175 YOD1 1598 g2441.t1 3426g6710.t1 7.528783 1.563904 −5.0227 −0.39468 −4.53706 0.006224 1599g6940.t1 3427 g6448.t1 0 6.016039 5.937675 −0.41441 4.523508 0.0063411601 g5186.t1 3429 g3777.t1 K02934: RP-L6e, 4.28578 0 −4.72311 −0.41768−4.52127 0.006349 RPL6 1600 g3254.t1 3428 g8225.t1 0 5.869262 5.544325−0.41746 4.521417 0.006349 1602 g2757.t1 3430 g9153.t1 K15053: CHMP7 02.528581 2.167777 −0.42072 4.519182 0.006365 1603 g8191.t1 3431 g9716.t12.640244 5.393849 2.932616 −0.42423 4.51677 0.006385 1604 g41.t1 2544g2830.t1 K10740: RPA3 5.456896 1.684193 −3.50612 −0.43149 −4.51180.006426 1605 g7930.t1 3432 g2853.t1 K01077: E3.1.3.1, 5.436852 2.710109−4.15755 −0.43376 −4.51024 0.006432 phoA, phoB 1606 g9899.t1 3433g3476.t1 0 5.790708 5.501572 −0.43434 4.509842 0.006432 1607 g6747.t13434 g4361.t1 K08793: STK32, 1.640577 7.804707 6.025167 −0.439124.506569 0.006449 YANK 1609 g3450.t1 3436 g4695.t1 K11319: ING3 7.7930561.832762 −5.3581 −0.44607 −4.50182 0.006476 1608 g13903.t1 3435 g687.t1K01426: E3.5.1.4, 2.308161 5.757553 3.146851 −0.44596 4.501889 0.006476amiE 1610 g4174.t1 3437 g1802.t1 K03164: TOP2 0 4.461914 4.257824−0.44926 4.499626 0.006485 1611 g1817.t1 3438 g1704.t1 K13941: folKP1.569971 6.747653 4.234672 −0.45137 4.498183 0.00649 1612 g16037.t1 3439g4108.t1 K01744: aspA 4.664569 6.76341 2.175875 −0.45455 4.4960070.006508 1613 g10914.t1 3440 g5925.t1 1.756741 4.535424 3.244364−0.46789 4.486892 0.006589 1614 g138.t1 3441 g3729.t1 4.847226 0.925828−5.03041 −0.47101 −4.48476 0.006598 1615 g2936.t1 3442 g5964.t1 8.0448940.248534 −6.73944 −0.47284 −4.4835 0.006601 1616 g8866.t1 3443 g2108.t1K13339: PEX6, 11.8966 2.107495 −8.86497 −0.48781 −4.47329 0.006671PXAAA1 1617 g4740.t1 3444 g2014.t1 K02606: ORC4 4.269663 1.432791−2.74295 −0.48799 −4.47317 0.006671 1618 g17490.t1 3445 g10534.t1K10777: LIG4, 1.37437 7.556488 5.810689 −0.48948 4.472145 0.006674 DNL41619 g6095.t1 3446 g7353.t1 10.01399 0.524763 −9.03171 −0.51858 −4.452310.006833 1620 g1092.t1 3447 g4035.t1 1.619955 5.721483 3.640435 −0.533624.442078 0.006907 1621 g12252.t1 3448 g235.t1 0.132439 3.243255 3.821541−0.53381 4.441948 0.006907 1622 g6796.t1 3449 g4421.t1 K03680: EIF2B45.126406 0.843849 −4.22061 −0.54287 −4.43579 0.006966 1623 g797.t1 3450g8161.t1 0 3.053206 2.866046 −0.55063 4.430521 0.007005 1624 g5647.t13451 g1105.t1 5.271321 0.695521 −5.99485 −0.556 −4.42687 0.007028 1625g15866.t1 3452 g9844.t1 2.040941 8.117785 5.437517 −0.57127 4.4165120.007114 1626 g6617.t1 3453 g11274.t1 K13953: adhP 9.164416 5.669006−3.74273 −0.57468 −4.41419 0.007135 1628 g6780.t1 3455 g4396.t1 4.3250361.1994 −3.75976 −0.57681 −4.41275 0.007142 1627 g5153.t1 3454 g3822.t11.244336 5.595008 3.814632 −0.57638 4.413043 0.007142 1629 g5834.t1 3456g1171.t1 K04393: CDC42 5.842709 0.801203 −4.48638 −0.5775 −4.412290.007142 1630 g5375.t1 3457 g9563.t1 6.246832 2.775505 −3.21809 −0.59214−4.40237 0.007231 1631 g10368.t1 3458 g5462.t1 K00826: E2.6.1.42,0.323199 4.887494 4.532182 −0.59353 4.401421 0.007232 ilvE 1632 g2826.t13459 g9093.t1 5.715948 1.969325 −4.3438 −0.60813 −4.39154 0.007312 1633g8263.t1 3460 g10014.t1 K09540: SEC63 1.178199 4.647047 3.105882−0.60945 4.390652 0.007317 1634 g1996.t1 3461 g6244.t1 0 2.1619442.537016 −0.61338 4.387995 0.007343 1636 g565.t1 3463 g3893.t1 7.2120954.016141 −3.8261 −0.62616 −4.37935 0.007416 1635 g10532.t1 3462 g6657.t10 6.423209 4.950366 −0.62535 4.379902 0.007416 1637 g9223.t1 3464g6550.t1 K14402: CPSF2, 4.757601 1.422654 −3.02304 −0.63182 −4.375530.007456 CFT2 1638 g4375.t1 3465 g2132.t1 K17777: TIM9 6.581887 2.288969−5.04428 −0.64088 −4.36942 0.007514 1639 g3924.t1 3466 g3968.t1 K03854:KTR 4.507947 8.80016 3.527047 −0.64187 4.368744 0.007517 1640 g5877.t13467 g10964.t1 1.237514 5.716716 4.577402 −0.65497 4.359912 0.0076091641 g7244.t1 3468 g10768.t1 1.270272 6.454926 4.671181 −0.66639 4.352210.007694 1642 g3215.t1 3469 g6111.t1 6.28213 1.918338 −4.18097 −0.67385−4.34719 0.007746 1643 g2744.t1 3470 g8873.t1 12.4437 4.004642 −6.34323−0.67665 −4.3453 0.007764 1644 g10172.t1 3471 g8453.t1 1.719814 6.9752624.867858 −0.67848 4.34407 0.007769 1646 g11998.t1 3473 g2455.t1 K01792:E5.1.3.15 4.113876 1.68217 −2.91764 −0.68435 −4.34012 0.007808 1645g9935.t1 3472 g6028.t1 0 5.001669 5.050202 −0.68376 4.340518 0.0078081647 g9810.t1 3474 g10828.t1 6.142355 2.944412 −3.12615 −0.68611−4.33894 0.007817 1648 g2585.t1 3475 g1533.t1 1.186682 5.314928 4.416457−0.70324 4.327418 0.007953 1649 g5812.t1 3476 g7683.t1 0.086084 5.7558755.49766 −0.70639 4.3253 0.00797 1650 g7613.t1 3477 g7623.t1 K12177:COPS3, 6.832706 1.20583 −6.6405 −0.71007 −4.32283 0.007995 S5N3 1651g21752.t1 3478 g11785.t1 9.138517 2.10622 −5.18056 −0.71052 −4.322530.007995 1652 g8125.t1 3479 g7937.t1 K14829: IPI3 5.635984 8.1656873.420929 −0.71501 4.319512 0.008023 1653 g1265.t1 3480 g446.t1 02.255216 2.515104 −0.72389 4.313556 0.008084 1654 g1851.t1 3481 g1893.t1K14806: DDX31, 4.180789 6.833176 3.613285 −0.72476 4.312968 0.008086DBP7 1655 g5970.t1 3482 g7911.t1 0.787727 4.745143 3.037594 −0.726414.311862 0.00809 1656 g9210.t1 3483 g432.t1 0 5.395553 4.999741 −0.729794.309594 0.008103 1657 g4885.t1 3484 g5284.t1 K00451: HGD, 2.7110219.250394 4.936597 −0.75813 4.290601 0.008322 hmgA 1658 g9727.t1 3485g1208.t1 0 2.707059 2.656284 −0.77155 4.281622 0.008405 1659 g1852.t13486 g1892.t1 9.129284 5.622142 −2.9499 −0.77281 −4.28078 0.008408 1661g4708.t1 3488 g2052.t1 5.134526 2.604627 −2.75857 −0.77636 −4.278410.008419 1662 g1264.t1 3489 g447.t1 K07975: K07975 0 3.433264 3.424199−0.77691 4.27804 0.008419 1660 g9176.t1 3487 g6513.t1 1.38307 7.0230375.604965 −0.77564 4.27889 0.008419 1663 g10978.t1 3490 g5642.t1 09.109111 6.49256 −0.77811 4.277239 0.00842 1664 g7775.t1 3491 g849.t15.558934 1.67851 −5.74356 −0.78625 −4.2718 0.008488 1665 g10472.t1 3492g2156.t1 1.835908 10.72995 8.679924 −0.80576 4.258766 0.008642 1666g11361.t1 3493 g11673.t1 K01613: psd, PISD 5.614261 0.835332 −3.65067−0.81024 −4.25578 0.008666 1667 g5499.t1 3494 g4955.t1 4.580901 7.4971462.894342 −0.81895 4.249973 0.008726 1668 g8184.t1 3495 g5029.t1 K05607:AUH 3.031275 0 −3.53658 −0.84752 −4.23094 0.008935 1669 g9878.t1 3496g11628.t1 K05755: ARPC4 0 8.072633 7.232249 −0.84945 4.229652 0.0089481670 g10675.t1 3497 g8521.t1 K00688: E2.4.1.1, 0.169628 5.7819375.478988 −0.85152 4.228278 0.008956 glgP, PYG 1671 g9232.t1 3498g3432.t1 K00545: COMT 7.296935 0.411124 −6.22613 −0.8545 −4.2263 0.008981672 g9988.t1 3499 g9675.t1 K00130: betB, 0 2.553591 3.110324 −0.862334.221089 0.009044 gbsA 1673 g1414.t1 3500 g6284.t1 2.311758 6.7175284.69322 −0.86385 4.220079 0.009053 1674 g6733.t1 3501 g4345.t1 K09043:AP1F 0 5.001212 4.248888 −0.86816 4.217209 0.00909 1675 g7043.t1 3502g6332.t1 5.859345 10.2543 4.890605 −0.88033 4.209124 0.009187 1676g2705.t1 3503 g8367.t1 K00528: E1.18.1.2, 7.551805 3.162022 −5.08662−0.88328 −4.20717 0.009204 fpr 1677 g10342.t1 3504 g51.t1 0 5.6785455.567869 −0.88506 4.205988 0.00921 1678 g5928.t1 3505 g11021.t1 K09885:AQPF 5.755454 0.419682 −5.37723 −0.89503 −4.19937 0.009274 1679 g8175.t13506 g7987.t1 1.51165 7.320745 5.975986 −0.89646 4.198423 0.009275 1680g8032.t1 3507 g4282.t1 0 4.127275 3.299567 −0.91209 4.188055 0.0093981681 g9814.t1 3508 g10824.t1 K03062: PSMC1, 1.362902 5.056672 3.336585−0.91516 4.186022 0.009415 RPT2 1682 g11969.t1 3509 g7462.t1 0.4895685.568038 4.427228 −0.91543 4.185844 0.009415 1683 g10790.t1 3510g10663.t1 0.828146 4.846815 3.562604 −0.92472 4.179692 0.009497 1684g4805.t1 3511 g1632.t1 8.950015 5.163246 −3.59682 −0.93185 −4.174970.009558 1685 g6554.t1 3512 g10090.t1 K15565: CTK3 5.222663 0.144855−4.83662 −0.93476 −4.17304 0.009576 1686 g1116.t1 3513 g4063.t1 1.0054295.625694 3.855418 −0.94482 4.16639 0.009663 1687 g8449.t1 3514 g2682.t1K05954: FNTB 0 5.399599 4.115948 −0.95049 4.162638 0.009697 1689g6525.t1 3516 g2064.t1 K09493: CCT1, 9.538137 1.667123 −6.73424 −0.95515−4.15956 0.009725 TCP1 1690 g5857.t1 3517 g1146.t1 K02320: POLA13.021693 6.891883 4.04023 −0.95542 4.159376 0.009725 1688 g1274.t1 3515g460.t1 0 6.05494 9.515249 −0.95514 4.159568 0.009725 1691 g12431.t13518 g10686.t1 K07127: uraH, 0 5.825339 4.833292 −0.95677 4.1584890.009733 pucM, hiuH 1692 g5322.t1 3519 g2238.t1 K03426: E3.6.1.22,5.48509 2.765673 −3.98262 −0.95893 −4.15706 0.009743 NUDT12, nudC 1693g10361.t1 3520 g7713.t1 2.118062 5.477606 3.633039 −0.96411 4.1536380.009765 1694 g2712.t1 3521 g8360.t1 6.902933 0.496994 −4.89563 −0.97385−4.1472 0.009833 1695 g6927.t1 3522 g6460.t1 K00485: FMO 9.6966661.489752 −6.7401 −0.98605 −4.13915 0.009945 1696 g6520.t1 3523 g2069.t17.419005 0.788997 −5.06498 −0.98929 −4.13702 0.009974 1697 g15004.t13524 g3115.t1 4.410253 0.439607 −3.37848 −0.99169 −4.13543 0.009991 1698g13717.t1 3525 g9904.t1 K01426: E3.5.1.4, 2.122753 4.721599 2.459777−0.99262 4.134823 0.009991 amiE 1699 g11731.t1 3526 g5851.t1 K00804:GGPS1 0.641201 8.014106 6.275604 −0.99873 4.130792 0.010032 1700g12319.t1 3527 g7427.t1 K06127: COQ5 0 3.18054 4.279183 −1.0114 4.1224450.010158 1037 g11120.t1 2520 g739.t1 K11309: RTT109, 4.245031 0.362852−4.44703 −1.02232 −4.11525 0.010262 KAT11 1701 g10208.t1 3528 g11172.t1K08737: MSH6 5.231935 0.620193 −4.43745 −1.02255 −4.11511 0.010262 1702g4510.t1 3529 g10815.t1 0.110413 4.81464 3.815621 −1.03144 4.1092550.010342 1703 g10697.t1 3530 g8542.t1 K01702: LEU1 0.263634 7.9125186.023521 −1.04447 4.100686 0.010463 1704 g15805.t1 3531 g2331.t1 K02154:0 2.888609 4.034147 −1.04529 4.100149 0.010465 ATPeV0A, ATP6N 1705g5031.t1 3532 g9002.t1 K02830: HRAD1, 3.089916 5.598348 2.991585−1.04815 4.098268 0.010485 RAD17 1706 g5436.t1 3533 g3139.t1 K16261: YAT5.060429 1.262422 −4.0977 −1.04901 −4.0977 0.010485 1707 g4238.t1 3534g1742.t1 1.066099 4.155929 2.917914 −1.053 4.09508 0.010521 1708g10868.t1 3535 g125.t1 0 3.653087 3.440687 −1.05442 4.094146 0.010531709 g6783.t1 3536 g4399.t1 6.220556 1.013936 −4.77542 −1.0556 −4.093370.010537 1710 g3062.t1 3537 g11769.t1 0 2.560725 2.204735 −1.060924.089879 0.010585 1711 g10221.t1 3538 g11208.t1 6.889613 0.40438−7.11534 −1.06965 −4.08415 0.010672 1712 g1829.t1 3539 g1715.t1 5.7917351.495617 −4.17043 −1.08999 −4.07081 0.010861 1713 g8326.t1 3540 g5128.t1K00505: TYR 3.610494 6.260581 3.534926 −1.09636 4.066632 0.010911 1714g3155.t1 3541 g4991.t1 3.59858 7.647083 3.797219 −1.11173 4.0565620.011074 1715 g2222.t1 3542 g11603.t1 0.225549 4.813511 4.351037−1.12206 4.049805 0.011164 1716 g11759.t1 3543 g10216.t1 3.685926 0−4.53515 −1.12292 −4.04924 0.011168 1717 g8206.t1 3544 g8502.t1 3.42071910.03021 6.493771 −1.1248 4.048012 0.011183 679 g4287.t1 2759 g1939.t1K00275: pdxH, 0.807563 3.090838 2.176492 −1.13595 4.040719 0.011299 PNPO690 g7926.t1 2497 g8597.t1 6.166677 8.61834 2.778981 −1.13847 4.0390730.011322 1718 g4064.t1 3545 g3254.t1 K00002: AKR1A1, 6.100438 1.079083−4.91125 −1.15384 −4.02903 0.01147 adh 1720 g5795.t1 3547 g4862.t1K00451: HGD, 3.591089 6.8767 2.956306 −1.15712 4.026889 0.011485 hmgA1719 g5609.t1 3546 g7533.t1 0.882686 5.320606 3.796705 −1.15678 4.0271120.011485 1721 g19766.t1 3548 g11689.t1 K08272: CAB39, 4.724331 1.509326−3.78959 −1.16405 −4.02236 0.011549 MO25 1722 g7985.t1 3549 g10231.t1 04.06043 3.846952 −1.16466 4.021964 0.01155 1723 g4377.t1 3550 g2134.t114.14762 6.168036 −7.54239 −1.1682 −4.01966 0.01158 1724 g10842.t1 3551g9831.t1 K15283: SLC35E1 3.417746 7.907833 4.552081 −1.17777 4.0134150.011665 1725 g3810.t1 3552 g5153.t1 K01539: ATP1A 5.831954 9.9759344.809042 −1.1815 4.010981 0.011698 1726 g4351.t1 3553 g2123.t1 2.9781885.643247 2.777696 −1.19302 4.003473 0.011817 1727 g12887.t1 3554g7811.t1 K03868: RBX1, 0 6.027624 4.370298 −1.19414 4.002739 0.011824ROC1 1728 g13707.t1 3555 g7796.t1 K04706: PIAS1 6.517298 4.766243−2.04941 −1.20773 −3.99389 0.011956 1729 g16831.t1 3556 g10344.t16.338633 1.444662 −4.08292 −1.20964 −3.99265 0.011974 1731 g3916.t1 3558g3976.t1 4.817018 0.75673 −4.65895 −1.22292 −3.98401 0.012097 1730g5660.t1 3557 g1082.t1 0 4.671882 3.638252 −1.22213 3.984518 0.0120971732 g9151.t1 3559 g6484.t1 6.278283 0.8931 −5.76977 −1.23184 −3.97820.012199 1733 g12202.t1 3560 g9295.t1 0.672484 4.169208 2.907439−1.23665 3.975077 0.012241 1734 g5282.t1 3561 g2288.t1 4.202468 0.654126−3.30483 −1.23744 −3.97457 0.012244 1735 g7572.t1 3562 g7669.t1 3.9786537.606234 3.70123 −1.2385 3.973875 0.012244 1736 g3235.t1 3563 g8210.t14.470468 8.184527 5.15127 −1.24494 3.969692 0.012307 697 g852.t1 2502g9454.t1 K11824: AP2A 4.880882 7.286171 2.290375 −1.24576 3.9691580.012307 1737 g6716.t1 3564 g4321.t1 9.948221 2.821953 −6.95531 −1.25354−3.9641 0.012386 1738 g2067.t1 3565 g2530.t1 7.69826 4.922109 −3.56419−1.26788 −3.95479 0.012535 1739 g7743.t1 3566 g7093.t1 2.175372 4.6179962.642137 −1.27196 3.95215 0.012576 1740 g5491.t1 3567 g9819.t1 9.3010852.365816 −5.52656 −1.27566 −3.94974 0.012619 1741 g10936.t1 3568g2319.t1 8.259645 1.32013 −5.22157 −1.27719 −3.94876 0.012632 939g4598.t1 2528 g6014.t1 4.80428 1.524453 −3.6354 −1.2848 −3.943820.012715 1742 g10549.t1 3569 g6695.t1 0 1.785939 2.000492 −1.295853.936658 0.012829 527 g4985.t1 2324 g8953.t1 0.777528 7.11879 6.4966−1.30752 3.929102 0.012948 578 g8174.t1 2376 g7986.t1 1.469754 6.1855034.308101 −1.31185 3.926293 0.012985 1743 g2143.t1 3570 g11929.t1 K00772:E2.4.2.28, 4.8374 0.969878 −3.56778 −1.3345 −3.91164 0.013284 mtaP 1744g9848.t1 3571 g9777.t1 K06970: rlmF 9.547112 5.371618 −3.97134 −1.34065−3.90767 0.013349 1745 g12220.t1 3572 g11110.t1 K07870: RHOT1, 3.8843026.478847 3.518086 −1.34423 3.905351 0.013393 ARHT1 1746 g2291.t1 3573g10709.t1 5.385805 9.526471 4.775916 −1.34937 3.902029 0.013444 1747g2147.t1 3574 g11880.t1 K14789: NOP6 6.507448 1.977499 −4.68012 −1.35307−3.89964 0.013467 1748 g6355.t1 3575 g794.t1 K00236: SDHC, 0.5368786.254053 4.787495 −1.36034 3.894946 0.013558 SDH3 1749 g2869.t1 3576g11261.t1 0.327373 6.340001 4.80532 −1.36591 3.891347 0.013632 1750g2360.t1 3577 g9254.t1 K12200: PDCD6IP, 3.801939 1.686361 −2.17748−1.36819 −3.88988 0.013658 ALIX, RIM20 1751 g3560.t1 3578 g3325.t16.818439 0.789095 −4.92675 −1.37135 −3.88784 0.013689 1752 g10589.t13579 g7032.t1 0 2.526539 3.338928 −1.37427 3.885952 0.013716 1753g16530.t1 3580 g8785.t1 4.610888 0.254363 −4.08665 −1.38154 −3.881260.013816 1754 g5177.t1 3581 g3786.t1 K03321: TC.SULP 4.026352 0.667334−3.40117 −1.38727 −3.87757 0.013878 1755 g9386.t1 3582 g3647.t1 K01082:E3.1.3.7, 7.430096 4.382531 −3.00795 −1.38737 −3.8775 0.013878 cysQ,MET22, BPNT1 1756 g6130.t1 3583 g7316.t1 K08657: TASP1 0.095949 5.5755095.53383 −1.38749 3.87743 0.013878 1757 g8530.t1 3584 g6289.t1 K05532:MNN11 0 5.816826 4.892278 −1.38966 3.876025 0.013899 1758 g21699.t1 3585g5541.t1 K03448: FEN2, 0.735044 3.625342 2.870907 −1.39176 3.8746730.013906 LIZ1 1759 g9934.t1 3586 g6029.t1 K16575: ACTR1, 0 5.8324055.597162 −1.39893 3.870056 0.013978 ARP1 1760 g4777.t1 3587 g3680.t13.32587 5.729749 2.411959 −1.4021 3.868009 0.014015 1761 g11542.t1 3588g4184.t1 7.517977 2.707186 −4.47011 −1.41398 −3.86036 0.014171 1762g2157.t1 3589 g11896.t1 3.702226 7.226007 3.353898 −1.41467 3.8599140.014174 1763 g16189.t1 3590 g1458.t1 K14454: GOT1 10.63207 6.499538−6.07526 −1.41542 −3.85943 0.014178 1764 g8348.t1 3591 g5159.t1 4.2644576.507615 2.242904 −1.41809 3.857714 0.014202 1765 g1259.t1 3592 g452.t12.440869 6.057593 3.423879 −1.42343 3.854274 0.01426 1766 g2764.t1 3593g9147.t1 K10745: 0 2.695204 3.586065 −1.42688 3.852056 0.014297 RNASEH2C1767 g7927.t1 3594 g8596.t1 4.918651 7.912131 3.059833 −1.4292 3.8505620.014312 1768 g2676.t1 3595 g4133.t1 K00294: E1.2.1.88 0.612742 5.410364.447987 −1.4294 3.850434 0.014312 1769 g7548.t1 3596 g7259.t1 0.6498675.412471 4.266032 −1.43441 3.847211 0.014366 1771 g5182.t1 3598 g3781.t19.026587 2.801517 −6.79697 −1.43708 −3.84549 0.014391 1770 g7942.t1 3597g9703.t1 2.085423 7.573442 5.338061 −1.43698 3.845559 0.014391 1772g4091.t1 3599 g3293.t1 K01687: ilvD 6.303323 0.815929 −5.63696 −1.43932−3.84405 0.014418 1773 g12310.t1 3600 g7399.t1 0 7.275303 5.468252−1.44443 3.840765 0.014489 1774 g3831.t1 3601 g2596.t1 K07005: K07005 04.871672 3.653881 −1.4486 3.838085 0.014546 1776 g3521.t1 3603 g2212.t1K10666: RNF5 4.087847 5.915388 2.294451 −1.45392 3.834664 0.014606 1775g22438.t1 3602 g4987.t1 5.797361 8.454162 3.989287 −1.45372 3.8347970.014606 1777 g4129.t1 3604 g1851.t1 3.118092 5.15901 2.22408 −1.454693.834169 0.01461 1778 g12080.t1 3605 g7812.t1 5.157342 0.417205 −5.18316−1.4566 −3.83294 0.014632 1779 g18095.t1 3606 g931.t1 5.760364 1.160199−6.11966 −1.45925 −3.83124 0.014666 1780 g2261.t1 3607 g10673.t14.246251 8.170102 5.158696 −1.46304 3.828806 0.014718 1781 g2951.t1 3608g5953.t1 K11129: NHP2, 4.43109 0.997175 −3.38379 −1.46821 −3.825480.014759 NOLA2 1782 g2355.t1 3609 g9249.t1 K07192: FLOT 6.8195851.646734 −5.57734 −1.47687 −3.81992 0.014873 1783 g3075.t1 3610g11781.t1 0 4.238844 3.140408 −1.48663 3.813664 0.014988 1784 g9642.t13611 g6905.t1 0 4.384934 5.279139 −1.48909 3.812083 0.015012 1786g7748.t1 3613 g7098.t1 K12815: DHX38, 1.598146 5.454032 3.568819−1.49259 3.809836 0.015052 PRP16 1785 g10300.t1 3612 g22.t1 0 4.9508924.957814 −1.49227 3.810047 0.015052 1787 g1381.t1 3614 g8684.t1 6.5374760 −5.14045 −1.49524 −3.80814 0.01508 1788 g3923.t1 3615 g3970.t15.651846 0.874231 −4.49336 −1.49537 −3.80806 0.01508 1789 g2286.t1 3616g10703.t1 K11362: HFIL 1.780691 5.389549 3.610777 −1.50303 3.8031440.015181 ADA1 692 g5169.t1 2506 g3798.t1 4.28203 6.198144 2.254081−1.50534 3.801665 0.01521 1790 g5917.t1 3617 g11006.t1 0.479676 3.3439782.923854 −1.5088 3.799443 0.01525 1791 g6287.t1 3618 g8349.t1 K11366:7.027226 0 −6.44608 −1.51412 −3.79604 0.01533 USP22_27_51, UBP8 1792g6643.t1 3619 g10197.t1 5.091815 1.733439 −3.47331 −1.51828 −3.793370.01539 1793 g12218.t1 3620 g11102.t1 2.315098 5.094179 2.505163−1.52401 3.789702 0.015468 1794 g7936.t1 3621 g11228.t1 K00232:E1.3.3.6, 4.459893 9.555022 5.227644 −1.52659 3.788048 0.015503 ACOX1,ACOX3 1795 g5748.t1 3622 g5250.t1 1.632799 4.080474 2.918063 −1.527963.787172 0.015518 1796 g9069.t1 3623 g8579.t1 0 6.161139 6.446955−1.53152 3.784889 0.01556 1797 g6312.t1 3624 g3007.t1 K05236: COPA5.253098 7.43545 2.144029 −1.54263 3.77778 0.0157 1799 g8177.t1 3626g7989.t1 9.520565 3.609284 −4.61836 −1.54631 −3.77543 0.015742 1798g14196.t1 3625 g5807.t1 K01754: E4.3.1.19, 5.027436 7.101036 2.225321−1.54586 3.775716 0.015742 ilvA, tdcB 1800 g6471.t1 3627 g5309.t1K11237: BEM1 8.657428 1.580264 −5.3132 −1.54781 −3.77447 0.015759 1801g8179.t1 3628 g7991.t1 K15450: TYW3 1.394748 4.160609 2.833287 −1.550613.772678 0.015798 1802 g6447.t1 3629 g5339.t1 0.745984 4.49131 3.550615−1.55175 3.771949 0.015808 1803 g4305.t1 3630 g1960.t1 K07179: RIOK22.332881 9.808031 7.49955 −1.56836 3.761323 0.016051 1804 g10921.t1 3631g2051.t1 3.554471 15.34968 12.40633 −1.5698 3.760406 0.016067 1805g7453.t1 3632 g6882.t1 K11230: SSK2 6.592207 0.47792 −6.24926 −1.57242−3.75873 0.016095 1806 g4994.t1 3633 g8965.t1 4.95489 0.379021 −5.0321−1.57389 −3.75779 0.016103 1807 g13512.t1 3634 g8777.t1 K07047: K07047 01.953187 2.809714 −1.57688 3.75588 0.016146 1808 g13145.t1 3635 g4288.t1K12795: SUGT1, 0 3.863111 4.262765 −1.57792 3.755218 0.016156 SGT1 1809g2403.t1 3636 g9304.t1 3.466706 5.880267 2.766617 −1.58819 3.7486580.0163 1810 g11546.t1 3637 g4179.t1 2.95634 4.859952 2.334894 −1.590773.747012 0.016337 1811 g6245.t1 2545 g7144.t1 3.519044 0.986255 −2.56971−1.59307 −3.74554 0.016351 1812 g20527.t1 3638 g9499.t1 0 2.4237813.298103 −1.5938 3.745074 0.016355 1814 g485.t1 3640 g5481.t1 3.2119340.513195 −3.05545 −1.59982 −3.74123 0.016427 1813 g9589.t1 3639 g6640.t1K14564: NO0P56 0 4.752235 3.463157 −1.59979 3.741252 0.016427 1815g17338.t1 3641 g4825.t1 3.253347 11.98725 6.42899 −1.60143 3.740210.016446 1816 g5556.t1 3642 g7468.t1 0.321853 8.712554 6.936626 −1.605943.737329 0.0165 683 g9852.t1 3089 g9791.t1 0.93993 4.257415 3.235897−1.61117 3.733993 0.016567 1817 g9592.t1 3643 g6324.t1 0 3.241194.466041 −1.61236 3.733234 0.01657 1818 g9909.t1 3644 g3464.t1 4.8990610.389899 −4.4519 −1.61774 −3.7298 0.016649 1819 g347.t1 3645 g8852.t1K01619: deoC, 5.001834 2.638493 −2.09583 −1.61831 −3.72944 0.01665 DERA1820 g3024.t1 3646 g8280.t1 K15183: ELL 4.940617 6.802739 2.356057−1.62092 3.727777 0.016675 1821 g3400.t1 3647 g10340.t1 4.5748348.898182 4.895081 −1.62268 3.726654 0.016684 1822 g5059.t1 3648 g8329.t1K15544: SSU72 3.885616 1.04666 −3.67463 −1.62812 −3.72318 0.016767 1823g13701.t1 3649 g7800.t1 K00227: SC5DL, 3.52458 8.32101 6.721913 −1.628263.723097 0.016767 ERG3 1824 g7883.t1 3650 g8666.t1 K17871: ndh1 8.9788214.745077 −4.2343 −1.62992 −3.72204 0.016789 1825 g9357.t1 3651 g4026.t11.461054 4.608619 3.269834 −1.64365 3.713291 0.017021 1826 g6504.t1 3652g10649.t1 K01487: E3.5.4.3, 3.115047 5.480797 3.226369 −1.64905 3.7098530.017102 guaD 1827 g996.t1 3653 g8065.t1 K03859: PIGC, 0 5.1640115.152798 −1.65445 3.70641 0.017175 GPI2 1828 g12072.t1 3654 g7819.t17.465114 4.358481 −4.43566 −1.66028 −3.7027 0.017256 1829 g8430.t1 3655g6112.t1 0 3.595832 4.134153 −1.664 3.700333 0.017293 1830 g1011.t1 3656g8080.t1 1.836426 5.321783 3.474028 −1.66832 3.697583 0.01736 1831g7418.t1 2549 g7203.t1 K17497: PMM 4.250746 0.725203 −3.91923 −1.6743−3.69378 0.017427 1832 g9496.t1 3657 g5757.t1 0.783088 6.487481 4.380159−1.67836 3.691201 0.017484 1833 g9186.t1 3658 g6518.t1 4.151632 10.487216.043581 −1.68184 3.688985 0.017532 1834 g7004.t1 3659 g6378.t1 K11229:BCK1 0 2.324218 2.253785 −1.68839 3.684823 0.017638 1836 g8143.t1 3661g7948.t1 4.054206 0.695466 −3.66885 −1.6899 −3.68386 0.017639 1835g11752.t1 3660 g9854.t1 K11086: SNRPB, 5.274986 2.280814 −3.12018−1.6896 −3.68405 0.017639 SMB 1837 g17537.t1 3662 g9665.t1 4.572358.898002 4.283534 −1.69297 3.681912 0.017688 1838 g5667.t1 3663 g1075.t14.489128 2.536094 −2.39358 −1.70341 −3.67528 0.017868 1839 g6664.t1 3664g2224.t1 K13525: VCP, 2.105221 5.652047 4.78303 −1.70384 3.6750050.017868 CDC48 1840 g2801.t1 3665 g9129.t1 7.466543 0.556432 −6.6491−1.70804 −3.67233 0.017928 1841 g4812.t1 3666 g9598.t1 4.049291 6.428792.167629 −1.70915 3.671628 0.017928 1843 g2466.t1 3668 g6718.t1 5.984030 −5.16123 −1.7182 −3.66588 0.018067 1842 g249.t1 3667 g11056.t1 K00276:AOC3, 5.423135 1.39377 −3.95337 −1.71813 −3.66593 0.018067 AOC2, tynA1844 g13312.t1 3669 g4520.t1 K01800: maiA, 0 2.734484 3.220496 −1.718433.665736 0.018067 GSTZ1 1845 g9893.t1 3670 g3483.t1 0 6.706192 4.976759−1.71907 3.665331 0.01807 1846 g17202.t1 3671 g3078.t1 5.68592 2.231786−3.83595 −1.72034 −3.66452 0.018076 1847 g5069.t1 3672 g8336.t1 K14521:NAT10, 0 3.583017 3.343135 −1.72847 3.659364 0.018188 KRE33 1848g7275.t1 3673 g11843.t1 0.251195 5.321335 4.264195 −1.7299 3.6584590.018207 1849 g4877.t1 3674 g4496.t1 0.134441 10.17863 6.723251 −1.731513.657431 0.018229 1850 g12737.t1 3675 g5715.t1 0 3.366893 5.496972−1.7331 3.656428 0.018251 1851 g3173.t1 3676 g11661.t1 3.672536 1.077381−2.65537 −1.73393 −3.6559 0.018258 1852 g4631.t1 3677 g2422.t1 2.3118834.745023 2.541357 −1.73959 3.652307 0.018351 1853 g601.t1 3678 g3857.t10 4.551928 4.659305 −1.74334 3.649928 0.018406 1854 g4634.t1 3679g2419.t1 5.63215 7.748538 2.895179 −1.74706 3.647572 0.018445 1855g13170.t1 3680 g1290.t1 K01620: ltaE 0 1.960601 3.162229 −1.747223.647467 0.018445 1856 g3136.t1 3681 g5050.t1 0 2.474936 2.012582−1.75162 3.644677 0.018519 1857 g14953.t1 3682 g1391.t1 3.3347246.021478 2.572465 −1.75216 3.644334 0.018519 1858 g11237.t1 3683g1362.t1 2.76252 5.104646 2.123089 −1.76267 3.637676 0.018659 1859g1833.t1 3684 g1913.t1 K03248: EIF3G 0 3.706133 3.037564 −1.764893.636266 0.018694 1860 g6040.t1 3685 g11728.t1 K16368: DGK1 9.6812712.587529 −5.33304 −1.7661 −3.6355 0.018707 1861 g11936.t1 3686 g10365.t14.454058 0.327662 −3.42743 −1.76646 −3.63527 0.018707 1862 g4010.t1 3687g8176.t1 K15427: SIT4, 5.918167 1.131513 −3.97297 −1.77022 −3.632890.018745 PPH1 1864 g3458.t1 3689 g4687.t1 2.234014 5.975139 2.819321−1.77233 3.631552 0.018756 1865 g4936.t1 3690 g4576.t1 0.924146 3.7168993.064721 −1.77306 3.631089 0.018756 1866 g1815.t1 3691 g1702.t1 2.6857976.479459 3.431879 −1.77314 3.63104 0.018756 1863 g7697.t1 3688 g11510.t11.950115 6.128154 4.639048 −1.77179 3.631893 0.018756 1867 g1592.t1 3692g12245.t1 0 4.518156 4.414945 −1.7816 3.62568 0.01888 1868 g9431.t1 3693g10302.t1 5.228093 0.705484 −5.82699 −1.78382 −3.62428 0.018915 1869g10761.t1 3694 g12006.t1 K15082: RAD7 3.567408 6.390408 2.846424 −1.79853.614981 0.01914 1870 g6898.t1 3695 g1355.t1 2.604143 5.101685 2.991821−1.80118 3.613286 0.019185 1871 g13109.t1 3696 g9757.t1 K01620: ltaE 02.071355 2.163561 −1.80694 3.609643 0.019256 1872 g1060.t1 3697 g8133.t14.616756 0.514584 −3.57327 −1.81051 −3.60738 0.019301 1873 g7618.t1 3698g7618.t1 2.193329 5.285081 3.154401 −1.81683 3.603386 0.019394 1874g1395.t1 3699 g6218.t1 3.913913 7.425386 3.628307 −1.82293 3.5995330.019503 1875 g1934.t1 3700 g10921.t1 6.270225 2.041068 −5.92102−1.82531 −3.59803 0.01953 1876 g10864.t1 3701 g114.t1 1.463031 4.9386653.973683 −1.82564 3.59782 0.01953 1877 g10895.t1 3702 g5900.t1 04.186104 3.125415 −1.8289 3.595755 0.019562 1878 g5532.t1 3703 g11340.t11.931855 7.130479 5.020293 −1.83514 3.591812 0.019672 1879 g7251.t1 3704g10776.t1 4.989318 0.254069 −3.57371 −1.85053 −3.58209 0.019932 1880g3894.t1 3705 g3998.t1 K00846: KHK 2.877684 5.230358 3.413778 −1.860073.576066 0.020088 1881 g819.t1 3706 g8183.t1 3.722054 7.412978 4.05158−1.86516 3.572854 0.020168 1882 g5100.t1 3707 g2942.t1 K06688: UBE2C, 01.914572 2.214387 −1.86814 3.570972 0.020216 UBC11 1883 g5175.t1 3708g3792.t1 K11498: CENPE 3.281173 0.222331 −4.74201 −1.88553 −3.560.020535 1884 g6483.t1 3709 g5291.t1 K13728: MAD2L2 1.918177 10.96487.40681 −1.89484 3.554125 0.020681 1885 g8029.t1 3710 g4279.t1 K01464:DPYS, 3.138026 5.812027 3.152124 −1.89915 3.551408 0.020756 dht, hydA1888 g1840.t1 3713 g1902.t1 4.350369 6.555403 3.614501 −1.90291 3.5490420.020781 1886 g5081.t1 3711 g8569.t1 K00505: TYR 0 4.71171 4.573953−1.9019 3.549673 0.020781 1887 g1692.t1 3712 g4651.t1 1.082713 6.1425334.604924 −1.90263 3.549214 0.020781 1889 g11007.t1 3714 g8699.t1 01.587767 2.088946 −1.90951 3.544881 0.020897 1890 g1760.t1 3715 g1200.t10 3.246854 2.445799 −1.91563 3.541022 0.021005 1891 g10371.t1 3716g10538.t1 0 4.965362 5.078563 −1.91874 3.539065 0.021065 1892 g7221.t13717 g5890.t1 5.661483 1.072226 −3.76681 −1.93127 −3.53117 0.021281 1893g6375.t1 3718 g771.t1 8.208151 3.648937 −4.25444 −1.93282 −3.530190.021294 1896 g2909.t1 3721 g6002.t1 1.238494 4.449583 3.244239 −1.935863.52828 0.021322 1894 g5154.t1 3719 g3823.t1 K17095: 3.505958 9.2836344.528734 −1.93535 3.528604 0.021322 ANXA7_11 1895 g20345.t1 3720g7516.t1 0 4.951177 4.852188 −1.93559 3.528453 0.021322 1897 g12606.t13722 g1144.t1 0 2.337207 2.424768 −1.94189 3.524487 0.02143 1898g7465.t1 3723 g6869.t1 3.054874 8.104242 4.242867 −1.94419 3.523040.021452 1899 g5267.t1 3724 g9694.t1 1.826832 5.783242 3.837809 −1.94913.519947 0.021535 1900 g4664.t1 3725 g2382.t1 5.504862 1.603502 −4.21381−1.95339 −3.51725 0.021593 1901 g17749.t1 2523 g12099.t1 7.5982919.839638 2.512479 −1.95532 3.516031 0.021628 1902 g6418.t1 3726 g5371.t1K03778: ldhA 2.853999 4.669676 2.946243 −1.95976 3.513237 0.021721 1903g10763.t1 3727 g12010.t1 K01209: E3.2.1.55, 2.945033 0 −3.29535 −1.96318−3.51109 0.02177 abfA 1904 g666.t1 3728 g9881.t1 4.362664 0.664419−3.76077 −1.96699 −3.50869 0.021838 1906 g1908.t1 3730 g8731.t1 2.2114550 −3.68585 −1.97784 −3.50187 0.022044 1907 g3413.t1 3731 g4733.t1K06902: UMF1 2.141863 7.189473 4.094946 −1.97792 3.501818 0.022044 1905g9155.t1 3729 g6487.t1 K02324: POLE1 4.234902 8.900666 4.422793 −1.977383.502159 0.022044 1908 g10394.t1 3732 g10563.t1 0 5.322562 4.509387−1.9801 3.50045 0.022075 1909 g7696.t1 3733 g11509.t1 0.601935 3.1075552.748423 −1.98765 3.495705 0.022202 1910 g2535.t1 3734 g3567.t1 K05758:ARPC2 11.15766 3.882187 −7.40548 −1.99331 −3.49215 0.022306 1911g8186.t1 3735 g7993.t1 K01079: serB, 4.063757 0.499721 −4.16492 −1.99443−3.49144 0.022322 PSPH 1912 g4471.t1 3736 g6834.t1 0.878562 4.7430263.759323 −1.99869 3.488764 0.022414 1913 g8237.t1 3737 g10043.t13.086194 5.293821 2.302039 −1.99973 3.488113 0.022418 1914 g9619.t1 3738g7243.t1 K11339: 0 2.363574 3.497394 −2.00042 3.487675 0.022424 MORF411,MRG15, EAF3 1915 g1911.t1 3739 g6147.t1 K08334: BECN1, 4.443069 1.325402−4.48934 −2.0025 −3.48637 0.022458 VPS30, ATG6 1916 g7540.t1 3740g7267.t1 K01179: E3.2.1.4 3.106323 7.044516 4.718377 −2.0027 3.4862470.022458 1917 g2857.t1 3741 g9061.t1 4.958463 1.63825 −3.2435 −2.00585−3.48427 0.022502 1918 g5306.t1 3742 g2255.t1 5.053243 1.769587 −3.06328−2.00736 −3.48332 0.022507 1919 g4916.t1 3743 g4552.t1 K13950: pabAB 04.100904 3.309752 −2.00896 3.482311 0.022524 1920 g7255.t1 3744g10781.t1 1.044041 5.343757 3.456906 −2.0128 3.479902 0.022607 1921g5468.t1 3745 g8430.t1 4.014859 1.728033 −2.2011 −2.02184 −3.474230.022807 1922 g10379.t1 3746 g10546.t1 K03507: DPB11 0 2.887983 2.329258−2.02243 3.473857 0.02281 1923 g2332.t1 3747 g9197.t1 K09484: QUIB,0.359609 4.730422 6.455702 −2.04055 3.462484 0.023216 qa-3 640 g12554.t12440 g3576.t1 K02953: RP-S13e, 6.593986 3.286592 −3.5936 −2.0451−3.45963 0.023319 RPS13 1924 g134.t1 3748 g5827.t1 6.48267 2.73113−3.87561 −2.04641 −3.4588 0.023339 1925 g6562.t1 3749 g10098.t1 K04627:STE3 6.840025 3.508287 −3.0943 −2.04677 −3.45858 0.023339 1926 g835.t13750 g8204.t1 5.9061 3.739419 −2.89332 −2.05738 −3.45193 0.023574 1927g3961.t1 3751 g3929.t1 K15631: ABA3 4.682251 0.610791 −4.20667 −2.05917−3.4508 0.023606 1928 g9090.t1 3752 g8544.t1 9.042656 3.394564 −4.42541−2.06054 −3.44994 0.023622 1929 g8220.t1 3753 g10063.t1 K11380: NTO10.981794 5.762532 4.770402 −2.06314 3.448316 0.023659 1930 g1688.t1 3754g4655.t1 3.67154 6.41277 3.431308 −2.06707 3.445853 0.02371 1931g10593.t1 3755 g7036.t1 0 1.637191 2.310481 −2.06843 3.444999 0.0237341932 g7454.t1 3756 g6881.t1 K13237: DECR2 7.244054 3.351771 −4.66071−2.07246 −3.44247 0.023826 1933 g1006.t1 3757 g8076.t1 5.641821 1.01679−5.33245 −2.07757 −3.43927 0.023924 1934 g558.t1 3758 g6454.t1 5.4687012.998081 −3.81423 −2.07899 −3.43838 0.02395 1935 g8492.t1 3759 g3364.t12.17787 5.143839 3.198935 −2.08565 3.434206 0.024077 1936 g3284.t1 3760g8263.t1 K04567: KARS, 0 3.096837 2.750146 −2.09247 3.429933 0.024176lysS 1937 g10375.t1 3761 g10542.t1 K18163: 0 3.09048 3.372823 −2.093833.429081 0.024189 NDUFAF6 1938 g9651.t1 3762 g6914.t1 8.216351 3.957187−3.97535 −2.09941 −3.42558 0.02429 1939 g6236.t1 3763 g7134.t1 1.928679.554801 7.372855 −2.10264 3.423559 0.024364 1940 g5143.t1 3764 g3836.t12.580565 8.674743 4.091749 −2.1038 3.422838 0.024383 1941 g11455.t1 3765g7021.t1 0.596448 5.043975 4.462447 −2.10687 3.420916 0.024452 1942g5389.t1 3766 g2429.t1 4.873893 0 −5.94573 −2.11075 −3.41849 0.0245431943 g6232.t1 3767 g7130.t1 6.918168 0.488136 −5.39134 −2.11243 −3.417430.024569 1944 g13866.t1 3768 g4613.t1 K15115: 0.791928 5.833256 4.134026−2.11257 3.417341 0.024569 SLC25A32, MFT 1945 g7546.t1 3769 g7261.t1K06113: abnA_B 1.693461 6.005734 3.98049 −2.11746 3.414282 0.024676 1946g10144.t1 3770 g8474.t1 K17086: 6.358648 2.274685 −5.01733 −2.12573−3.40911 0.024862 TM9SF2 4 1947 g8973.t1 3771 g11361.t1 K08496: GOSR2, 03.168015 2.664668 −2.12811 3.407616 0.024915 BOS1 1948 g5708.t1 3772g2670.t1 3.903218 6.617966 3.389449 −2.13389 3.403997 0.025048 1950g6963.t1 3774 g6427.t1 K14408: CSTF3, 6.941008 0 −5.14398 −2.13547−3.40301 0.025067 RNA14 1949 g15819.t1 3773 g6469.t1 6.143278 2.028742−3.66691 −2.13542 −3.40304 0.025067 1951 g9667.t1 3775 g4881.t1 K18757:LARP1 1.474494 5.026138 3.073674 −2.13624 3.40253 0.025072 1952g12694.t1 3776 g8901.t1 0 4.059599 3.514485 −2.13747 3.401759 0.0250871953 g3429.t1 3777 g4716.t1 K10755: RFC2_4 6.366861 3.029398 −4.00095−2.13997 −3.4002 0.02512 1954 g4582.t1 3778 g4118.t1 1.381451 5.6262834.430383 −2.14063 3.399781 0.025126 1955 g3157.t1 3779 g4989.t1 3.1008878.957858 6.174002 −2.15214 3.392585 0.025381 1956 g82.t1 3780 g2764.t1K17422: MRPL41 0 6.458967 4.487087 −2.15351 3.391728 0.025396 1957g624.t1 3781 g11304.t1 0.779024 4.503237 2.584446 −2.15576 3.3903220.025427 1958 g1143.t1 3782 g253.t1 0 4.407125 4.086029 −2.16257 3.386060.025587 1959 g6371.t1 3783 g780.t1 K08287: E2.7.12.1 2.726445 7.3926155.376711 −2.17655 3.377322 0.025905 1960 g1751.t1 3784 g9723.t1 2.7953345.572355 3.187095 −2.17894 3.375831 0.025959 1961 g4236.t1 3785 g1745.t14.004311 6.248441 2.562026 −2.18036 3.374942 0.025987 1962 g8695.t1 3786g11550.t1 4.911201 1.458168 −3.1977 −2.18135 −3.37432 0.026004 859g490.t1 2536 g5492.t1 K01230: MAN1 3.341994 5.830489 2.819683 −2.183293.37311 0.026046 1963 g5421.t1 3787 g5085.t1 8.070442 0.46074 −5.99862−2.18759 −3.37042 0.026135 1964 g2502.t1 3788 g3530.t1 K13288: orn, 04.539539 4.217905 −2.18823 3.370025 0.026138 REX2, REXO2 1965 g2567.t13789 g5735.t1 4.150469 7.075168 2.267847 −2.19188 3.367744 0.026205 1966g4811.t1 3790 g9600.t1 3.984392 2.169587 −2.35064 −2.19298 −3.367060.026224 1967 g6775.t1 3791 g4391.t1 K18748: SSD1 7.196236 1.868572−5.15477 −2.20272 −3.36098 0.026429 1969 g10391.t1 3793 g10558.t1 05.449561 5.122671 −2.21155 3.35546 0.026586 1968 g1041.t1 3792 g8112.t1K11227: PBS2 0 5.802497 5.568864 −2.2107 3.355987 0.026586 1971g11559.t1 3795 g4170.t1 5.952815 2.501869 −3.41726 −2.21296 −3.354580.026603 1970 g13704.t1 3794 g11109.t1 1.780391 5.388679 3.682525−2.21285 3.354646 0.026603 1972 g3779.t1 3796 g2656.t1 0 2.294593.055708 −2.21449 3.353624 0.026623 1973 g2737.t1 3797 g9165.t1 8.1118673.708757 −3.11076 −2.21608 −3.35263 0.026657 1974 g6644.t1 3798g10196.t1 0.529024 4.052835 2.69518 −2.21902 3.350793 0.026706 1975g9251.t1 3799 g10432.t1 6.615159 0.815708 −4.57198 −2.2196 −3.350430.02671 1977 g5146.t1 3801 g3831.t1 1.613274 5.642097 3.424626 −2.222553.348593 0.026759 1976 g7543.t1 3800 g7264.t1 1.778839 6.311218 3.7799−2.22228 3.348757 0.026759 1978 g7853.t1 3802 g10510.t1 K15306: RANBP1 01.987939 2.649547 −2.22545 3.34678 0.026819 1979 g7747.t1 3803 g7097.t1K14791: PWP1 1.814601 4.202941 2.631876 −2.22599 3.346441 0.026823 1980g3283.t1 3804 g8262.t1 K11400: ARP4 0 2.989351 3.88489 −2.22752 3.3454920.026855 1981 g3579.t1 3805 g3304.t1 K00472: 3.489594 9.820105 6.138885−2.22818 3.345078 0.026862 E1.14.11.2 1982 g4997.t1 3806 g8967.t11.989279 5.409008 3.503902 −2.2339 3.341506 0.026993 1983 g466.t1 3807g8012.t1 4.101739 6.505153 2.812413 −2.23476 3.34097 0.027006 1984g3042.t1 3808 g1617.t1 K01638: E2.3.3.9, 4.286461 1.427891 −2.69449−2.23709 −3.33952 0.027061 aceB, glcB 1985 g2105.t1 3809 g2480.t1K12189: VPS25, 5.392127 1.688441 −3.98468 −2.24246 −3.33617 0.027171EAP20 1986 g10030.t1 3810 g3456.t1 K03952: NDUFA8 4.085114 0.317024−3.2909 −2.24726 −3.33317 0.027263 1987 g10020.t1 3811 g10918.t1 K01238:E3.2.1.- 0 2.377597 3.865002 −2.24806 3.332671 0.027274 1988 g6440.t13812 g9393.t1 1.856577 5.779447 3.68737 −2.25497 3.328362 0.027454 1989g10867.t1 3813 g124.t1 0 4.39728 4.400864 −2.25581 3.32784 0.027467 1990g3799.t1 3814 g863.t1 5.870835 2.857198 −2.27046 −2.25914 −3.325760.027534 1991 g10346.t1 3815 g44.t1 K18328: DBR1 0 2.241769 3.604053−2.25968 3.325424 0.027534 1992 g9896.t1 3816 g3480.t1 0 5.4179735.231502 −2.25972 3.325396 0.027534 1993 g7695.t1 3817 g11508.t1 K01640:E4.1.3.4, 0.184849 4.606471 4.094707 −2.26451 3.322414 0.02764 HMGCL,hmgL 1994 g851.t1 3818 g9450.t1 7.233882 2.603782 −3.98752 −2.26621−3.32135 0.027678 1995 g13873.t1 3819 g4607.t1 K14845: RAI1, 1.753375.060998 3.620071 −2.27209 3.317686 0.027818 DOM3Z 1996 g5244.t1 3820g2347.t1 K02877: RP-L15e, 4.414688 11.84847 5.818625 −2.27366 3.3167080.027853 RPL15 1997 g13106.t1 3821 g9753.t1 K01892: HARS, 0 2.2091282.453035 −2.27519 3.315751 0.027886 hisS 1998 g11726.t1 3822 g5854.t15.938268 0.538037 −5.1103 −2.27837 −3.31377 0.02796 1999 g2723.t1 3823g9178.t1 4.416635 0.748978 −3.32728 −2.28414 −3.31017 0.028107 2000g5988.t1 3824 g11687.t1 6.638403 4.410083 −2.22473 −2.28525 −3.309480.028129 2001 g6939.t1 3825 g6449.t1 K01560: E3.8.1.2 1.458794 5.7935474.011947 −2.29299 3.304659 0.028315 2003 g13415.t1 3827 g8381.t1 K00618:E2.3.1.1 5.219776 7.979734 3.470781 −2.29519 3.303285 0.028357 2002g37.t1 3826 g2834.t1 K02926: RP-L4, 1.828605 4.71647 4.723031 −2.295193.303285 0.028357 MRPL4, rplD 2004 g3662.t1 3828 g651.t1 0.8724276.371311 4.041603 −2.29616 3.302681 0.028362 2005 g9235.t1 3829 g3428.t10 3.972927 4.57957 −2.29616 3.302679 0.028362 2006 g7674.t1 3830g7572.t1 5.466518 2.783883 −4.32184 −2.29711 −3.30209 0.028368 2007g4036.t1 3831 g3210.t1 4.501248 0.83444 −3.4584 −2.29717 −3.302050.028368 2008 g5276.t1 3832 g2295.t1 4.938586 0.923903 −3.91412 −2.30002−3.30028 0.028406 2009 g11802.t1 3833 g12042.t1 3.076257 6.4718183.398775 −2.30107 3.299622 0.028426 2010 g9414.t1 3834 g3612.t1 6.6238753.522539 −4.17633 −2.30173 −3.29921 0.028434 656 g16181.t1 2457g12075.t1 K08257: 5.57367 2.794291 −3.13674 −2.30477 −3.29731 0.028477E3.2.1.101 2012 g10897.t1 3836 g5902.t1 0 2.586402 2.018878 −2.304473.297501 0.028477 2011 g7210.t1 3835 g5874.t1 K09780: K09780 1.1143883.993513 3.261747 −2.30435 3.297579 0.028477 2013 g4453.t1 3837 g6809.t15.118903 0.695521 −6.34745 −2.31256 −3.29247 0.028643 2014 g606.t1 3838g3853.t1 K16261: YAT 3.858126 5.880152 2.075602 −2.32021 3.2876980.028843 2015 g4470.t1 3839 g6833.t1 1.147637 5.898161 3.859584 −2.32483.284838 0.028961 2016 g6738.t1 3840 g7868.t1 5.417721 3.126867 −3.45553−2.32976 −3.28175 0.029069 2017 g9769.t1 3841 g939.t1 K15326: TSEN542.152088 5.841014 4.075185 −2.33059 3.281231 0.029079 2018 g8609.t1 3842g3035.t1 K11684: BDF1 5.659852 2.072019 −3.03129 −2.33159 −3.280610.029098 2019 g7209.t1 3843 g5873.t1 1.535387 3.753918 2.595474 −2.333553.279388 0.029145 2020 g9079.t1 3844 g7839.t1 3.237265 5.083271 2.50233−2.33749 3.276937 0.029238 2021 g488.t1 3845 g5490.t1 5.069028 0.661124−3.94585 −2.33858 −3.27626 0.02924 2022 g11121.t1 3846 g740.t1 1.0951745.476241 3.763338 −2.33866 3.276212 0.02924 2023 g7270.t1 3847 g11833.t1K01649: leuA 0.794723 4.590596 3.756172 −2.34295 3.27354 0.029292 2024g8493.t1 3848 g3365.t1 3.869494 6.395043 2.369665 −2.35653 3.2650840.029712 2025 g9798.t1 3849 g10841.t1 K04564: SOD2 6.169922 3.581629−3.17615 −2.35997 −3.26294 0.029809 2026 g4827.t1 3850 g711.t1 3.1381235.609277 2.266361 −2.36209 3.261622 0.029865 2027 g7690.t1 3851 g7594.t1K09705: K09705 6.512504 2.963367 −3.48703 −2.3645 −3.26012 0.029917 2028g6785.t1 3852 g4403.t1 K06111: EXOC4, 7.141887 3.434524 −3.10329−2.36545 −3.25954 0.029935 SEC8L1 2029 g11719.t1 3853 g2321.t1 4.1220112.09891 −3.55772 −2.36866 −3.25754 0.030026 2030 g4828.t1 3854 g712.t15.692735 2.652303 −3.51649 −2.37281 −3.25496 0.030122 2031 g942.t1 3855g9313.t1 K09241: GAL4 1.854413 3.96608 2.304511 −2.37691 3.2524040.030229 2032 g11848.t1 3856 g8790.t1 2.601552 0.409353 −2.22171−2.37796 −3.25175 0.030251 2033 g21824.t1 3857 g7394.t1 0 5.235343.655249 −2.38527 3.247202 0.030464 2034 g2821.t1 3858 g11279.t15.756117 3.458502 −2.0711 −2.3872 −3.24601 0.030515 2035 g6696.t1 3859g11145.t1 K09704: K09704 7.789281 2.074215 −5.24082 −2.38775 −3.245660.03052 2036 g4155.t1 3860 g1823.t1 K18551: SDT1 5.022148 1.693257−2.97251 −2.38832 −3.2453 0.030526 2037 g9766.t1 3861 g942.t1 3.2129658.164358 4.327837 −2.39337 3.242162 0.030679 2039 g13908.t1 3863g8736.t1 3.218518 0.78025 −2.44992 −2.39434 −3.24156 0.030685 2038g9809.t1 3862 g10829.t1 3.118004 5.544287 2.518375 −2.39418 3.241660.030685 2040 g6787.t1 3864 g4405.t1 1.161527 5.099231 3.21425 −2.397143.239817 0.030752 2041 g9405.t1 3865 g3622.t1 3.567627 5.477382 2.497615−2.40468 3.23513 0.030977 2042 g2509.t1 3866 g3539.t1 K11874: UBP161.872531 5.493777 3.650258 −2.4068 3.233811 0.031035 2043 g5355.t1 3867g9.t1 2.290026 0.356189 −2.03022 −2.40761 −3.23331 0.031049 2044g4497.t1 3868 g10803.t1 4.996184 7.333602 3.047979 −2.4116 3.2308320.031143 2045 g8224.t1 3869 g10058.t1 3.041354 5.822561 3.713464−2.41714 3.227386 0.031264 2046 g4940.t1 3870 g4580.t1 2.195152 8.6039975.13217 −2.41716 3.227371 0.031264 2047 g3634.t1 3871 g611.t1 K08331:ATG13 3.988422 0.822981 −3.37249 −2.42114 −3.2249 0.031385 2048 g228.t13872 g11036.t1 K14833: NOC2 5.004033 8.298645 2.944132 −2.43094 3.2188050.031692 2049 g48.t1 3873 g2823.t1 K01433: purU 2.612144 5.7419833.012018 −2.43232 3.217947 0.031713 2050 g281.t1 3874 g11374.t1 9.378794.604117 −4.12735 −2.43274 −3.21769 0.031713 2051 g12734.t1 3875g5711.t1 K11662: ACTR6, 0 2.30116 2.840219 −2.43365 3.217125 0.031718ARP6 2052 g10764.t1 3876 g12011.t1 K01581: E4.1.1.17, 5.248823 0.219074−4.66848 −2.4346 −3.21653 0.031737 ODC1, speC, speF 2053 g3828.t1 3877g2599.t1 K00505: TYR 0.869044 5.111409 3.294953 −2.43787 3.2144990.031836 2054 g1137.t1 3878 g246.t1 5.271354 1.818388 −3.65818 −2.43939−3.21355 0.031875 2055 g4066.t1 3879 g3252.t1 3.515498 1.112324 −2.46994−2.44069 −3.21275 0.031906 2056 g10836.t1 3880 g9834.t1 0.6214393.119334 2.691703 −2.44409 3.210636 0.03201 2057 g5068.t1 3881 g8335.t1K14685: SLC40A1, 0 7.218235 6.29332 −2.44716 3.208723 0.032062 FPN1 2058g9620.t1 3882 g7242.t1 K01648: ACLY 0 3.90929 3.533252 −2.45537 3.2036260.032253 2059 g5229.t1 3883 g2363.t1 5.943001 0.548669 −5.4291 −2.46004−3.20072 0.032375 2060 g8605.t1 3884 g3038.t1 4.532655 1.818868 −2.9624−2.46055 −3.20041 0.032379 2061 g10730.t1 3885 g2912.t1 K01469: OPLAH, 02.379516 2.107655 −2.46555 3.1973 0.032541 OXP1, oplAH 2062 g4774.t13886 g3677.t1 K15631: ABA3 9.027659 4.836111 −4.01499 −2.46683 −3.19650.032572 2063 g4508.t1 3887 g10813.t1 0.165642 5.824528 5.711017−2.46786 3.195865 0.032595 2064 g2571.t1 3888 g5739.t1 0.293052 8.0851374.840508 −2.46935 3.194939 0.03262 2065 g5434.t1 3889 g3137.t1 5.1430511.033474 −3.99467 −2.47101 −3.19391 0.032665 2066 g1199.t1 3890 g353.t1K02895: RP-L24, 6.44631 2.830134 −5.33548 −2.4716 −3.19354 0.032672MRP124, rplX 2067 g7868.t1 3891 g10526.t1 K02915: RP-L34e, 5.8494231.765368 −4.55948 −2.47674 −3.19035 0.032826 RPL34 2068 g1161.t1 3892g269.t1 5.46016 3.009009 −2.38008 −2.48667 −3.18418 0.033056 2070g4445.t1 3894 g6797.t1 4.844189 2.596249 −3.82423 −2.48854 −3.183020.033082 2069 g10124.t1 3893 g92.t1 4.215995 9.33502 4.637226 −2.488253.1832 0.033082 2071 g3873.t1 3895 g4021.t1 2.22259 5.09223 2.889394−2.49175 3.181028 0.033179 2072 g2508.t1 3896 g3536.t1 0 6.0707244.543999 −2.49201 3.18087 0.033179 2073 g8450.t1 3897 g2681.t1 02.871722 2.959236 −2.4972 3.177646 0.033351 2074 g7865.t1 3898 g10523.t17.879406 5.602482 −4.36688 −2.51011 −3.16963 0.033735 2075 g6937.t1 3899g6455.t1 K13108: SNIP1 0.333353 7.112752 4.778096 −2.51256 3.1681110.033811 2076 g4596.t1 3900 g6012.t1 K12855: PRPF6, 1.297068 7.6361615.013494 −2.51413 3.167137 0.033854 PRP6 2077 g16131.t1 3901 g11950.t1K00616: E2.2.1.2, 4.139806 0.380959 −2.80605 −2.51525 −3.16644 0.033861talA, talB 2078 g465.t1 3902 g8013.t1 K14325: RNPS1 0.1118 6.3475176.203301 −2.51547 3.166303 0.033861 2079 g1164.t1 3903 g270.t1 0.3182163.991449 5.225959 −2.51682 3.165462 0.033883 2080 g2408.t1 3904 g9480.t1K18550: ISN1 5.538089 8.86782 4.347478 −2.51899 3.164117 0.033935 2082g16130.t1 3906 g7073.t1 4.225688 6.146706 2.4124 −2.52079 3.1630020.033945 937 g8077.t1 2540 g7846.t1 6.655406 8.379386 2.917067 −2.520443.163218 0.033945 2081 g5524.t1 3905 g1651.t1 1.597727 5.655543 3.534574−2.5205 3.163177 0.033945 2083 g13129.t1 3907 g7779.t1 3.365795 1.169273−2.39087 −2.52343 −3.16136 0.034028 2084 g10991.t1 3908 g5657.t1 K12627:LSM8 0 2.170848 3.541712 −2.52601 3.159761 0.034109 2085 g1929.t1 3909g6163.t1 K01930: FPGS 2.613598 6.785311 3.342673 −2.52742 3.1588840.034147 523 g10740.t1 2319 g11987.t1 0 2.813231 2.132602 −2.527983.15854 0.034153 2086 g11974.t1 3910 g12283.t1 K01537: E3.6.3.8 4.460778.720128 4.497107 −2.52922 3.15777 0.034185 2087 g2386.t1 3911 g9282.t12.552078 5.80107 2.857308 −2.52973 3.157452 0.03419 2088 g11089.t1 3912g1541.t1 2.958185 5.916026 3.473746 −2.53269 3.155612 0.034271 549g6123.t1 2346 g7324.t1 9.721609 0 −6.70978 −2.53776 −3.15247 0.0344172089 g2879.t1 3913 g9507.t1 1.588916 5.963453 4.232111 −2.53843 3.1520520.034428 2090 g13476.t1 3914 g8719.t1 4.855623 0.713258 −4.14789−2.54165 −3.15005 0.034492 2091 g10480.t1 3915 g1680.t1 5.35355 2.766663−3.30455 −2.54237 −3.1496 0.034504 2092 g8013.t1 3916 g3404.t1 5.0491130.484288 −4.63964 −2.54362 −3.14883 0.034537 2093 g4367.t1 3917 g3791.t1K03448: FEN2, 5.072018 0.779082 −3.52579 −2.54647 −3.14707 0.034587 LIZ12094 g6987.t1 3918 g10858.t1 0.511756 5.093495 4.425198 −2.549123.145416 0.034644 2095 g10431.t1 3919 g8407.t1 K14861: URB1 9.4129612.402632 −4.79559 −2.55 −3.14487 0.034663 2096 g8248.t1 3920 g10031.t1K17424: MRPL43 1.653332 7.208956 3.793246 −2.55139 3.144009 0.0347012097 g9278.t1 3921 g112.t1 5.376359 0.900471 −5.07129 −2.5543 −3.142210.034795 561 g1198.t1 2358 g352.t1 K04513: RHOA 2.185924 5.5994313.115826 −2.56335 3.136592 0.03508 2098 g7656.t1 3922 g7539.t1 9.4842913.272208 −4.44358 −2.56665 −3.13455 0.035163 2099 g9071.t1 3923 g8570.t10 4.308308 2.935063 −2.5715 3.131534 0.035295 2100 g2276.t1 3924g10693.t1 K12761: SNF1 5.01028 6.964651 2.286462 −2.57593 3.1287880.035431 2101 g14507.t1 3925 g11494.t1 K01187. malZ 7.827356 5.131373−2.97808 −2.5835 −3.12409 0.03565 2102 g4366.t1 3926 g2127.t1 3.1083340.378977 −3.23784 −2.58635 −3.12232 0.035746 2103 g5569.t1 3927 g7488.t12.55743 5.105776 2.804623 −2.58922 3.120544 0.035842 2104 g12588.t1 3928g2936.t1 5.341725 1.287142 −4.50731 −2.59295 −3.11823 0.035935 2106g192.t1 3930 g5819.t1 0 4.078839 3.742625 −2.5932 3.118072 0.035935 2105g935.t1 3929 g9324.t1 1.589025 6.970304 5.205593 −2.59295 3.1182260.035935 2107 g7460.t1 3931 g6874.t1 K18176: COA3 0.679443 8.1327166.326235 −2.59401 3.117572 0.035941 2108 g2807.t1 3932 g3734.t1 K01053:E3.1.1.17, 6.975277 3.879255 −3.8776 −2.59679 −3.11585 0.036035 gnl, RGN2109 g4435.t1 3933 g6774.t1 3.295348 5.340307 2.156098 −2.59927 3.1143080.036117 2110 g9401.t1 3934 g3633.t1 K12668: OST2, 5.100436 7.0997163.045005 −2.60147 3.112946 0.036176 DAD1 2111 g1263.t1 3935 g448.t1K17421: MRPL40 0 5.570752 4.940149 −2.60151 3.112921 0.036176 2112g3490.t1 3936 g2182.t1 K03350: APC3, 5.226216 7.504737 2.341709 −2.603323.111795 0.036225 CDC27 2113 g10916.t1 3937 g267.t1 3.408478 5.6334643.418244 −2.60479 3.110889 0.036225 2114 g921.t1 3938 g9342.t1 K18045:SIW14, 0 3.596272 3.808042 −2.60499 3.11076 0.036225 OCA3 2116 g7478.t13940 g6858.t1 4.55802 0.837774 −3.42667 −2.61758 −3.10295 0.036604 2115g1744.t1 3939 g9730.t1 K16261: YAT 2.444031 4.709166 2.258978 −2.617553.102974 0.036604 2117 g10207.t1 3941 g11173.t1 K17866: DPH2 6.9807750.764559 −4.05418 −2.62021 −3.10133 0.036689 2118 g11843.t1 3942g8773.t1 K00993: EPT1 3.000341 0.893639 −2.21354 −2.62048 −3.101160.036689 2119 g3656.t1 3943 g636.t1 8.879204 5.164409 −2.89019 −2.62535−3.09814 0.03685 2120 g4331.t1 3944 g1983.t1 4.236756 1.896176 −3.14722−2.62618 −3.09762 0.036854 2121 g10256.t1 3945 g7194.t1 4.2093440.708524 −3.33023 −2.62967 −3.09546 0.036938 2122 g9189.t1 3946 g6521.t1K05663: 0.18774 5.583284 5.054504 −2.63044 3.09498 0.036954 ABC.ATM 2123g9587.t1 3947 g6638.t1 K02976: RPS526e, 0 3.89404 2.743634 −2.632193.093898 0.037009 RPS26 2124 g3483.t1 3948 g2152.t1 K00472: 0 4.0191653.218586 −2.63269 3.093584 0.037015 E1.14.11.2 2125 g4515.t1 3949g10820.t1 10.17358 3.683757 −4.93347 −2.6337 −3.09296 0.03704 2126g5855.t1 3950 g1148.t1 K12874: AQR 0 3.592743 3.462488 −2.63616 3.0914330.037124 2127 g11080.t1 3951 g1560.t1 K13303: SGK2 3.663667 5.6398522.488524 −2.63746 3.090627 0.03716 2128 g17161.t1 3952 g9655.t1 3.9467766.251222 2.716762 −2.63779 3.090423 0.03716 2129 g913.t1 3953 g9352.t13.761447 1.842695 −2.6974 −2.64185 −3.08791 0.037284 2131 g4992.t1 3955g8962.t1 5.568434 1.070393 −4.64888 −2.64356 −3.08685 0.037304 2130g5921.t1 3954 g11009.t1 0.726064 3.654951 2.376852 −2.64348 3.0868960.037304 2132 g10214.t1 3956 g11973.t1 4.391352 5.888419 2.232265−2.64574 3.085498 0.037377 2134 g1192.t1 3958 g2652.t1 7.331953 0−4.76693 −2.64809 −3.08404 0.037428 2133 g5409.t1 3957 g8611.t1 0.4871216.397764 4.771873 −2.64784 3.084192 0.037428 2135 g6619.t1 3959g11272.t1 K11159: K11159 10.02313 7.677217 −2.84367 −2.64911 −3.083410.037454 2136 g5978.t1 3960 g11675.t1 K01187: malZ 4.632559 1.508608−2.55697 −2.65074 −3.0824 0.037506 2137 g9539.t1 3961 g6568.t1 K05906:PCYOX1, 0 3.166553 5.702237 −2.6513 3.082052 0.037513 FCLY 2138g13602.t1 3962 g10129.t1 K09579: PIN4 3.22586 7.700999 4.342095 −2.654563.080031 0.037601 2139 g10588.t1 3963 g7031.t1 0 5.84847 4.399222−2.65698 3.078527 0.03767 2140 g8167.t1 3964 g7975.t1 4.268879 6.3626383.264487 −2.66061 3.076281 0.037775 2141 g6658.t1 3965 g10210.t11.079636 5.470349 3.827162 −2.66129 3.07586 0.037784 2142 g1881.t1 3966g4234.t1 K01725: cynS 4.230103 2.82032 −2.77283 −2.66619 −3.072820.037943 2143 g11727.t1 3967 g5855.t1 3.728683 0.656698 −2.85634−2.66698 −3.07233 0.03796 2144 g3432.t1 3968 g4712.t1 K00505: TYR 03.109455 4.733726 −2.67446 3.067691 0.038224 2145 g20186.t1 3969g6363.t1 5.012816 7.163425 2.999714 −2.68527 3.060993 0.038598 2146g447.t1 3970 g8029.t1 K13431: SRPR 4.802134 1.949645 −2.92415 −2.69849−3.0528 0.039107 2147 g4444.t1 3971 g6795.t1 4.899102 2.093375 −3.84401−2.69952 −3.05216 0.039136 2148 g18374.t1 3972 g7684.t1 K12856: PRPF8,4.95726 1.392127 −3.87785 −2.70169 −3.05082 0.039186 PRP8 2149 g8150.t13973 g7956.t1 K02959: RP-S16, 5.17122 2.06327 −3.42667 −2.70179 −3.050760.039186 MRPS16, rpsP 2150 g1210.t1 3974 g364.t1 5.549737 1.972661−3.45578 −2.70577 −3.04829 0.039324 2151 g8164.t1 3975 g7965.t1 0.2649326.326912 4.484822 −2.71181 3.044544 0.039565 2153 g8665.t1 3977 g2654.t14.448871 0 −4.40278 −2.71535 −3.04235 0.039644 2154 g6421.t1 3978g5368.t1 3.418022 7.778884 4.446548 −2.71542 3.04231 0.039644 2152g7000.t1 3976 g6384.t1 K15109: 0 5.827294 5.75825 −2.71486 3.0426550.039644 SLC25A20_29, CACT, CACL, CRC1 2155 g3832.t1 3979 g2595.t11.491655 5.211867 3.871807 −2.71908 3.040044 0.039755 2156 g10272.t13980 g2373.t1 6.233817 2.342297 −5.51583 −2.72027 −3.03931 0.039778 2158g4169.t1 3982 g1810.t1 2.732171 7.333986 3.584184 −2.72283 3.0377190.039793 2157 g10739.t1 3981 g11986.t1 0 3.441589 3.584342 −2.722693.037804 0.039793 2159 g5894.t1 3983 g10982.t1 K03030: PSMD14, 5.2358110 −4.2666 −2.72651 −3.03544 0.039906 RPN11, POH1 2160 g3017.t1 3984g8289.t1 4.253797 2.232303 −2.01665 −2.72969 −3.03347 0.040028 2161g2235.t1 3985 g10642.t1 0 8.944426 6.651699 −2.73008 3.033226 0.0400292162 g444.t1 3986 g8037.t1 5.926244 1.755078 −4.43879 −2.73748 −3.028640.040289 2163 g8162.t1 3987 g7962.t1 2.242593 6.181948 2.975066 −2.74143.026215 0.04044 2164 g3781.t1 3988 g2653.t1 0 5.388341 4.391813−2.74166 3.026051 0.04044 2165 g446.t1 3989 g8030.t1 1.248806 3.1961432.232547 −2.74479 3.024112 0.040546 2166 g8813.t1 3990 g11548.t14.479092 1.564747 −2.31147 −2.75228 −3.01947 0.040844 2168 g484.t1 3992g5480.t1 K01083: E3.1.3.8 6.104152 1.195312 −3.75188 −2.76953 −3.008790.041524 2167 g6382.t1 3991 g762.t1 K11578: ZW10 4.043617 7.2461123.318946 −2.76929 3.008933 0.041524 2169 g13874.t1 3993 g4606.t12.192003 4.933315 3.081033 −2.77099 3.007879 0.04156 2170 g9768.t1 3994g940.t1 1.599958 5.142409 3.111563 −2.77117 3.00777 0.04156 2171g7100.t1 3995 g5567.t1 3.101236 4.623123 2.647789 −2.77245 3.0069740.041602 2172 g7685.t1 3996 g7577.t1 4.579641 1.059627 −4.79509 −2.77348−3.00633 0.041632 2174 g6166.t1 3998 g9581.t1 K10844: ERCC2, 3.6125696.046916 2.409001 −2.77444 3.005738 0.041644 XPD 2173 g20840.t1 3997g5601.t1 K09958: K09958 0 3.295785 3.355548 −2.77424 3.005865 0.0416442175 g4928.t1 3999 g4568.t1 K10752: RBBP4, 0.721987 4.891137 3.366959−2.7761 3.004716 0.041686 HAT2, CAF1, MIS16 2177 g4731.t1 4001 g2023.t13.62063 8.542099 3.637606 −2.78256 3.000712 0.041947 2178 g6999.t1 4002g6385.t1 0 5.909998 6.710453 −2.78479 2.999326 0.041984 2179 g1200.t14003 g354.t1 K03189: ureG 3.906083 6.287127 3.500283 −2.78517 2.9990910.041985 2180 g894.t1 4004 g9381.t1 1.98344 3.689145 2.509227 −2.786452.9983 0.042011 2181 g4606.t1 4005 g11246.t1 6.888917 0.934867 −4.17521−2.7892 −2.9966 0.04212 2182 g5836.t1 4006 g1169.t1 K01078: E3.1.3.24.897435 0.540874 −3.08894 −2.78981 −2.99622 0.042132 2183 g6795.t1 4007g4420.t1 K00620: argJ 1.412783 6.285553 3.554814 −2.7905 2.9957890.042148 2184 g13700.t1 4008 g7801.t1 K06666: TUP1 4.676696 9.1109535.842219 −2.79358 2.993881 0.042237 2185 g4127.t1 4009 g1853.t1 6.8830913.151116 −3.23591 −2.79424 −2.99347 0.042238 2186 g3498.t1 4010 g2189.t1K00888: PI4K 4.387206 8.035595 3.806841 −2.79735 2.991549 0.042365 2187g922.t1 4011 g9339.t1 0.335414 5.594 3.51525 −2.80783 2.985057 0.0428322188 g2095.t1 4012 g2498.t1 2.312071 5.547566 3.491828 −2.8095 2.9840220.042893 2189 g3886.t1 4013 g4006.t1 0.369905 5.31491 3.411646 −2.812932.981892 0.04302 2191 g2907.t1 4015 g4478.t1 K01361: 2.736066 5.918643.746675 −2.81508 2.980564 0.043087 E3.4.21.96 2190 g4132.t1 4014g1848.t1 3.459488 8.742363 3.852241 −2.8149 2.980673 0.043087 2192g102.t1 4016 g2922.t1 K15628: PXA 4.533487 1.423633 −3.06092 −2.81692−2.97942 0.043124 2193 g22195.t1 4017 g11335.t1 5.038549 3.116899−3.18678 −2.82113 −2.97682 0.043256 2194 g6067.t1 4018 g11760.t12.556856 5.057211 2.182582 −2.82589 2.973866 0.043414 2195 g7479.t1 4019g6857.t1 6.476209 0.753273 −5.14745 −2.82832 −2.97236 0.043492 2196g6849.t1 4020 g1428.t1 K14312: NUP155 5.863337 2.74764 −3.23983 −2.8286−2.97218 0.043492 2197 g6740.t1 4021 g4353.t1 3.814661 6.39705 3.411605−2.83035 2.971099 0.043559 2198 g1017.t1 4022 g8086.t1 1.006221 4.4620382.793294 −2.83106 2.970664 0.043575 2199 g20453.t1 4023 g7824.t1 02.0793 2.784209 −2.83156 2.970353 0.043583 2200 g1014.t1 4024 g8083.t1K13577: 2.388955 4.532509 2.338145 −2.83672 2.967153 0.04381 SLC25A10,DIC 2201 g3487.t1 4025 g2179.t1 0 3.411165 3.277123 −2.83823 2.9662190.04385 2202 g3156.t1 4026 g4990.t1 3.806958 6.990748 5.291192 −2.842272.963714 0.043975 2203 g21845.t1 4027 g8491.t1 0 2.721806 3.270562−2.84342 2.963002 0.044014 2204 g2266.t1 4028 g10682.t1 4.8670233.323245 −2.83067 −2.84548 −2.96173 0.044069 2205 g11688.t1 4029g10852.t1 3.032144 0.893416 −2.19305 −2.85456 −2.9561 0.044448 2206g6381.t1 4030 g763.t1 5.116653 0.131962 −3.22317 −2.85525 −2.955670.044464 2208 g10499.t1 4032 g1661.t1 4.339082 6.042177 2.559442−2.85649 2.954904 0.044491 2207 g17551.t1 4031 g8157.t1 K00558: DNMT1,2.888377 6.949835 3.089797 −2.85616 2.955108 0.044491 dcm 2209 g5340.t14033 g9534.t1 0.545456 7.258622 4.798642 −2.85837 2.953743 0.044548 2210g5285.t1 4034 g2285.t1 2.96395 7.10547 3.24264 −2.85885 2.9534440.044555 2211 g7357.t1 4035 g10412.t1 5.528929 0.619143 −3.97539−2.86359 −2.95051 0.044734 2213 g726.t1 4037 g10236.t1 0.483715 2.688772.384127 −2.86588 2.949088 0.044811 2212 g3514.t1 4036 g2206.t1 K11397:EAF1, 1.206815 6.642767 4.853325 −2.86574 2.949177 0.044811 VID21 2214g7257.t1 4038 g10783.t1 1.642966 6.188124 2.989166 −2.87117 2.9458130.045035 2215 g10215.t1 4039 g11972.t1 2.58645 7.403204 4.385523−2.87151 2.945602 0.045035 2216 g12395.t1 4040 g9538.t1 5.8610092.002652 −3.8787 −2.87539 −2.9432 0.045174 2217 g341.t1 4041 g8842.t15.788696 9.05636 2.247676 −2.87854 2.941243 0.045312 2218 g2488.t1 4042g3515.t1 K06669: SMC3, 1.945941 7.641363 3.740235 −2.88255 2.9387610.045473 CSPG6 2219 g713.t1 4043 g9934.t1 5.331222 0.664695 −4.38202−2.88525 −2.93708 0.045565 2220 g3763.t1 4044 g2673.t1 5.825851 3.254634−2.56829 −2.88539 −2.937 0.045565 2221 g7424.t1 4045 g7209.t1 5.3730929.386519 3.006451 −2.88618 2.93651 0.04557 2222 g5043.t1 4046 g10906.t1K01426: E3.5.1.4, 2.242898 6.456313 3.847076 −2.89168 2.933101 0.045808amiE 2223 g7402.t1 4047 g7184.t1 5.091428 2.484421 −2.06938 −2.89544−2.93077 0.045911 2224 g6538.t1 4048 g10076.t1 K12830: SF3B3, 0 3.0927633.060265 −2.90278 2.926225 0.046243 SAP130, RSE1 2225 g10909.t1 4049g5917.t1 2.072461 4.929452 2.681301 −2.90454 2.92513 0.046314 2226g10722.t1 4050 g4266.t1 K12827: SF3A3, 3.415338 6.31204 3.035059−2.90712 2.923532 0.046427 SAP61, PRP9 2227 g4840.t1 4051 g4450.t13.23602 0.449458 −3.90188 −2.91106 −2.92109 0.046537 2228 g1066.t1 4052g8139.t1 K01922: PPCS, 1.857534 4.106673 3.234378 −2.91469 2.9188410.046689 coaB 2229 g6576.t1 4053 g10109.t1 3.964575 0 −4.86543 −2.91615−2.91794 0.046745 2230 g107.t1 4054 g2928.t1 K03539: RPP1, 3.1979670.803547 −2.46999 −2.92305 −2.91366 0.047038 RPP30 2231 g3425.t1 4055g4720.t1 K02605: ORC3 6.578091 4.722727 −2.20212 −2.92326 −2.913530.047038 2232 g1018.t1 4056 g8087.t1 K04565: SOD1 2.947764 8.6807125.056988 −2.92384 2.913169 0.04705 2234 g5391.t1 4058 g2427.t1 3.7938260.942173 −4.97661 −2.92597 −2.91185 0.047091 2233 g7764.t1 4057 g879.t13.456716 1.497029 −2.42385 −2.92569 −2.91203 0.047091 506 g8644.t1 2302g2276.t1 K01166: E3.1.27.1 0 10.03085 6.401697 −2.92547 2.91216 0.0470912236 g1094.t1 4060 g4037.t1 K02358: tuf, 7.685682 5.149397 −2.8793−2.93139 −2.90849 0.047263 TUFM 2235 g712.t1 4059 g9943.t1 2.5637757.171783 3.80414 −2.93127 2.908563 0.047263 2237 g2419.t1 4061 g11542.t10.666287 3.962309 2.387936 −2.93259 2.907749 0.047307 2238 g2608.t1 4062g9643.t1 K00135: gabD 1.638785 4.294982 3.144001 −2.93448 2.9065750.047387 2239 g8147.t1 4063 g7952.t1 K11246: SHO1 6.066325 2.713104−3.95602 −2.93607 −2.90559 0.047433 2240 g5705.t1 4064 g10360.t10.642825 4.418076 3.166773 −2.93679 2.905146 0.047433 2241 g1222.t1 4065g374.t1 2.642618 5.883278 3.175464 −2.93706 2.90498 0.047433 2242g8664.t1 4066 g3812.t1 7.432168 1.550855 −4.57283 −2.93851 −2.904080.04749 2243 g4764.t1 4067 g1994.t1 6.940047 1.130412 −4.17201 −2.93963−2.90338 0.047531 2244 g6851.t1 4068 g1427.t1 2.284011 3.932777 2.957195−2.94037 2.902925 0.047551 2245 g10946.t1 4069 g5078.t1 K11236: CDC244.982918 0.83865 −3.5024 −2.94195 −2.90195 0.047598 2246 g1752.t1 4070g9722.t1 2.831268 5.535026 2.675068 −2.94838 2.897963 0.047896 2247g566.t1 4071 g3892.t1 K14708: 0.609198 5.65481 3.423398 −2.951462.896054 0.048021 SLC26A11 2248 g3553.t1 4072 g3337.t1 5.206188 1.970138−6.17884 −2.95714 −2.89253 0.048268 2249 g383.t1 4073 g7452.t1 K03978:engB 3.305487 5.192025 2.780869 −2.95719 2.892499 0.048268 2250 g7722.t14074 g3091.t1 K03014: RPB6, 0 4.540834 4.042193 −2.96294 2.8889360.048493 POLR2F 2251 g5453.t1 4075 g3167.t1 4.7696 0.934559 −3.55662−2.96747 −2.88612 0.048686 2252 g9542.t1 4076 g6565.t1 K01381: 03.886173 3.681133 −2.969 2.885177 0.048749 E3.4.23.25 2254 g1347.t1 4078g3449.t1 K01273: 4.946987 0.532441 −3.43411 −2.972 −2.88332 0.048837E3.4.13.19, DPEP1 2253 g4317.t1 4077 g1977.t1 2.161002 7.174394 3.592405−2.97197 2.883339 0.048837 2255 g5426.t1 4079 g3123.t1 K09539: DNAJC197.936931 3.022359 −5.07555 −2.97281 −2.88282 0.048862 2256 g22408.t14080 g9317.t1 K05351: E1.1.1.9 0 5.279355 4.074546 −2.97436 2.8818520.048927 2257 g6391.t1 4081 g5410.t1 K00480: 10.39213 2.102041 −5.87521−2.97645 −2.88056 0.048977 E1.14.13.1 2258 g4848.t1 4082 g4461.t15.837897 1.338468 −3.27267 −2.97698 −2.88023 0.048977 2259 g5255.t1 4083g2333.t1 5.719887 4.103219 −2.31021 −2.97885 −2.87907 0.049041 2261g10716.t1 4085 g11754.t1 4.124991 1.869399 −2.24701 −2.98266 −2.876710.049173 2260 g5384.t1 4084 g9571.t1 K13099: CD2BP2, 0 5.725959 3.979521−2.98264 2.876724 0.049173 PPP1R59 2262 g2819.t1 4086 g9111.t1 K16066:ydfG 5.823181 2.29085 −5.24434 −2.98895 −2.87281 0.049421 2265 g10820.t14089 g5705.t1 1.446801 4.641792 2.923813 −2.99351 2.869978 0.049577 2263g10158.t1 4087 g8462.t1 0 2.396169 3.866683 −2.9926 2.870543 0.0495772264 g844.t1 4088 g9461.t1 0 4.027461 4.070888 −2.99313 2.8702180.049577 2267 g2834.t1 4091 g9028.t1 4.114412 0.517908 −3.11219 −2.99494−2.8691 0.0496 2266 g10485.t1 4090 g1675.t1 0 4.900393 4.371976 −2.994842.869153 0.0496 2268 g11904.t1 4092 g11956.t1 K00681: ggt 3.2889980.166182 −3.64625 −2.99768 −2.86739 0.049713 2269 g21731.t1 4093g6097.t1 2.691539 0.619933 −4.08621 −3.00053 −2.86563 0.049849 2270g1202.t1 4094 g356.t1 K14768: UTP7, 1.026847 3.791611 2.583054 −3.003012.864088 0.049957 WDR46 2271 g9859.t1 4095 g11476.t1 0 4.020067 4.04691−3.00328 2.863921 0.049957 This table describes orthologous genes ofAcremonium zea sp. with beneficial and neutral effects on soybeangrowth, these genes show significant changes in expression between thetwo genotypes when grown in culture with soybean homogenate. “MedianExp. SYM00577” represents the median expression value in log2 tpm acrossbiological replicates of the beneficial Acremonium grown in mediainoculated with soybean seedling homogenate extracted with 50 mM PBS.“Median Exp. SYM003000” represents the median expression value in log2tpm across biological replicates of the neutral Acremonium grown inmedia inoculated with soybean seedling homogenate extracted with 50 mMPBS. “Log FC” represents the estimate of the log2-fold-change of thecontrast. “B- statistic” represents the log-odds that the gene isdifferentially expressed, “t-statistic” represents the moderatedt-statistic. “Adj. p-value” represents the false discovery rate(Benjamini & Hochberg, 1995) adjusted p-values.

TABLE 603 This table describes orthologous genes of Acremonium zea sp.with beneficial and neutral effects on soybean growth, these genes showsignificant changes in expression between the two genotypes when grownin culture without soybean homogenate. Median Median SEQ ID sym577 SEQID sym300 Exp. Exp. B- t- Adj. SYM00577 gene SYM00300 gene DescriptionSYM00577 SYM00300 Log FC statistic statistic p-value 687 g13072.t1 2494g9142.t1 0 8.254570732 8.205162 7.709718 15.19085 5.97E−06 700 g10575.t12526 g10634.t1 0 5.044729998 5.210069 5.708895 10.76568 2.93E−05 674g5345.t1 2555 g9530.t1 K03510: POLI 5.845894518 0.825824927 −4.700745.191774 −9.95863 4.34E−05 688 g68.t1 2495 g909.t1 K00106: XDH7.003820996 1.8413995 −4.97725 5.089442 −9.80948 4.75E−05 701 g12045.t12524 g804.t1 K12393: AP1M 6.653853259 0.902872062 −5.9827 4.978805−9.65176 5.17E−05 702 g1230.t1 2527 g388.t1 0 5.088279289 4.7076244.928839 9.581698 5.38E−05 703 g2767.t1 2559 g9144.t1 K02139: 02.891582245 2.883676 4.49609 9.003087 8.38E−05 ATPeFF, ATP17 704g7900.t1 2560 g8630.t1 6.140021427 2.188447902 −4.35168 4.123845−8.54179 0.000127 686 g857.t1 2491 g9451.t1 K01950: 3.8025146018.452816333 4.967614 4.058607 8.464065 0.000136 E6.3.5.1, NADSYN1, QNS1,nadE 675 g5348.t1 2554 g1.t1 0 4.361478247 4.207187 3.745443 8.1028580.000183 705 g10859.t1 2552 g120.t1 K17842: carT, 0 4.099415046 4.0010253.630507 7.974961 0.000207 CAO-2 706 g8300.t1 2561 g5097.t1 K15136:SRB5, 7.025134642 2.609740762 −4.37343 3.601634 −7.94321 0.000212 MED18707 g2262.t1 2562 g10678.t1 K11205: GCLM 0 6.497290601 5.707041 3.49627.828495 0.000234 708 g8448.t1 2563 g2683.t1 K00966: GMPP 0 11.294610449.891677 3.448641 7.777378 0.000245 709 g10027.t1 2564 g3454.t1 02.522819857 2.630813 3.252018 7.570029 0.00029 517 g13099.t1 2313g8761.t1 0 7.516860158 7.229 2.98496 7.298142 0.000373 710 g1584.t1 2517g2859.t1 7.332050712 1.763743187 −5.35718 2.961709 −7.27498 0.00038 690g7926.t1 2497 g8597.t1 6.853860482 1.736488111 −4.94929 2.879288−7.19348 0.000407 711 g9140.t1 2565 g6474.t1 K02434: gatB, 7.897012431.054868326 −8.62274 2.615828 −6.93929 0.000517 PET112 558 g9065.t1 2355g8585.t1 K03234: EEF2 0 1.996511676 2.075046 2.565361 6.891657 0.000539712 g3334.t1 2566 g4792.t1 0 2.790411134 2.620375 2.511141 6.8408430.000565 713 g3376.t1 2567 g10478.t1 0 2.519717879 2.387448 2.411896.748785 0.000619 714 g9.t1 2568 g3899.t1 0 4.899566565 4.1396042.330919 6.674579 0.000663 692 g5169.t1 2506 g3798.t1 4.8658182680.928859379 −3.94891 2.315037 −6.66012 0.00067 685 g6380.t1 2492 g764.t1K05857: PLCD 5.073855922 0.295559632 −4.51752 2.290181 −6.63754 0.000686696 g3920.t1 2508 g3972.t1 5.062011561 0.848055404 −4.26687 2.268441−6.61786 0.0007 715 g10569.t1 2569 g8038.t1 0 2.348179343 2.4817252.246454 6.598008 0.000711 716 g4884.t1 2570 g5157.t1 3.4936729047.387448493 4.164462 2.159094 6.519689 0.000767 717 g12587.t1 2571g2937.t1 5.143110791 1.384010569 −3.67942 1.930876 −6.31914 0.000935 718g9196.t1 2572 g6530.t1 K01937: pyrG, 2.877811039 6.539766193 3.9101871.874559 6.270516 0.000984 CTPS 719 g5920.t1 2573 g11008.t1 K02894:2.351855506 0 −2.24072 1.759813 −6.17247 0.001088 RP-L23e, RPL23 720g5591.t1 2547 g7515.t1 5.584485038 0.894846762 −4.42228 1.658568−6.08708 0.001189 721 g7216.t1 2574 g5885.t1 4.657263756 1.441622985−3.3104 1.633153 −6.0658 0.001218 722 g4371.t1 2575 g2128.t1 5.5102824950 −4.44208 1.572778 −6.01551 0.001275 698 g657.t1 2503 g9863.t14.4628192 1.558896118 −3.19078 1.546359 −5.99361 0.001305 723 g5419.t12576 g5084.t1 8.315874976 0.383504801 −6.22029 1.532513 −5.982160.001318 724 g5712.t1 2577 g1012.t1 5.583909958 0.874379809 −5.055121.414511 −5.88532 0.001468 725 g5938.t1 2578 g8896.t1 0 3.1780528823.1153 1.380226 5.857421 0.001515 726 g2504.t1 2579 g3532.t1 02.743866247 2.530417 1.349556 5.832557 0.001563 727 g7969.t1 2580g10252.t1 K03639: 4.758242645 8.67938655 4.03496 1.313775 5.8036570.001613 MOCS1, moaA 728 g1770.t1 2581 g1188.t1 6.058400928 1.675692023−4.12482 1.299312 −5.79201 0.001627 729 g815.t1 2582 g8179.t17.400064361 4.320735935 −3.01739 1.245211 −5.74859 0.001712 730 g3624.t12583 g600.t1 K14297: 5.106519345 1.117898542 −4.15716 1.207594 −5.718560.001762 NUP98, ADAR2 731 g3218.t1 2584 g6107.t1 4.600691335 0.295759975−4.21399 1.185637 −5.70109 0.001799 732 g6563.t1 2585 g10099.t17.052996504 3.472329984 −3.5087 1.155325 −5.67703 0.001844 733 g5058.t12586 g8328.t1 6.170884433 0 −5.05686 1.131697 −5.65833 0.001884 734g2063.t1 2587 g2535.t1 K01426: 6.62697264 2.303932777 −4.90902 1.127765−5.65523 0.001886 E3.5.1.4, amiE 735 g7620.t1 2588 g9046.t1 1.4697909224.894808598 3.487075 1.017153 5.568359 0.002056 737 g8108.t1 2590g7917.t1 5.22299962 2.496100539 −2.7244 0.995641 −5.55158 0.002086 736g13149.t1 2589 g42761 0 3.748353789 3.251627 0.996266 5.552068 0.002086738 g15293.t1 2591 g6106.t1 2.346160706 0.097742219 −2.19296 0.994155−5.55042 0.002087 739 g10986.t1 2592 g5652.t1 K02141: 0 4.4940395625.038067 0.963629 5.526686 0.002143 ATPeFH, ATP14 740 g2758.t1 2593g9152.t1 K10627: 0 4.883694275 4.299834 0.927171 5.498432 0.002209 RAD18741 g4882.t1 2594 g4502.t1 6.687936705 3.543460499 −3.27253 0.888456−5.46854 0.00228 742 g1999.t1 2595 g6250.t1 0 3.201001736 3.2273740.878381 5.460786 0.002292 743 g3555.t1 2596 g3333.t1 K01624: FBA,4.536933474 1.134755003 −3.43033 0.868413 −5.45312 0.002307 fbaA 744g4741.t1 2597 g2013.t1 K03237: EIF2S1 6.043892772 1.31228389 −4.402250.830737 −5.42421 0.002375 745 g5254.t1 2598 g2334.t1 K02137,5.144250658 2.18981705 −3.00766 0.818268 −5.41466 0.002395 ATPeF0O,ATP5O, ATP5 746 g5568.t1 2529 g7485.t1 2.950253937 7.105767696 4.1263790.80081 5.401317 0.002438 747 g19199.t1 2599 g12080.t1 K01102: PDP4.719048671 1.219706529 −3.83331 0.756008 −5.36718 0.002518 748 g4710.t12600 g6681.t1 K03457: 5.545619928 1.014147489 −4.86358 0.686637 −5.314630.002646 TC.NCS1 749 g1003.t1 2601 g8072.t1 K03626: EGD2, 9.5447251295.108026741 −4.51544 0.681969 −5.3111 0.002652 NACA 750 g12699.t1 2602g8909.t1 0 6.189343256 5.968321 0.664673 5.298059 0.00269 751 g3631.t12603 g607.t1 5.634764008 1.594206545 −4.0374 0.625713 −5.26876 0.00276752 g10888.t1 2604 g176.t1 K00463: INDO 0 4.02637883 3.250628 0.6104655.257326 0.002793 697 g852.t1 2502 g9454.t1 K11824: AP2A 5.5137952792.276512626 −3.03289 0.608594 −5.25592 0.002796 753 g10211.t1 2605g11976.t1 6.236601553 2.916440322 −3.19554 0.597045 −5.24728 0.002823754 g158.t1 2606 g5219.t1 0 5.582396377 5.11116 0.592518 5.2438870.002833 755 g6128.t1 2607 g7318.t1 K13953: adhP 0.559800663 7.1278192775.646838 0.588484 5.24087 0.002836 691 g5563.t1 2493 g7478.t14.371792513 0 −4.207 0.547655 −5.2104 0.002938 756 g5223.t1 2608g3707.t1 K03515: REV1 7.079279048 1.723275185 −5.46022 0.54628 −5.209370.00294 680 g1340.t1 2553 g523.t1 5.657989905 2.558100341 −3.776270.53802 −5.20322 0.002955 757 g6031.t1 2609 g11529.t1 K01885: EARS,8.997952533 1.491025779 −7.37296 0.51175 −5.18369 0.003013 gltx 758g5074.t1 2610 g2984.t1 0 6.655679639 7.343952 0.499918 5.174915 0.003026759 g6741.t1 2611 g4354.t1 2.11282087 5.448500076 4.101199 0.4961685.172135 0.003035 760 g829.t1 2612 g8197.t1 K13577: 0 6.8494057246.555104 0.494322 5.170766 0.003039 SLC25A10, DIC 761 g7264.t1 2613g11828.t1 5.499599524 1.415264641 −4.13804 0.465403 −5.14936 0.003123762 g2074.t1 2614 g2522.t1 4.591860791 7.078833392 3.299493 0.459635.145095 0.003137 763 g9395.t1 2615 g3638.t1 K06116: GPP1 2.3232917497.447835109 4.197994 0.459465 5.144973 0.003137 764 g9849.t1 2616g9778.t1 9.223686565 4.691855389 −4.09505 0.428461 −5.1221 0.003216 765g11803.t1 2617 g12043.t1 2.387616958 6.765913108 4.656261 0.3942115.096913 0.003318 766 g11916.t1 2618 g661.t1 7.715759124 1.189911629−6.35022 0.3901 −5.09389 0.003321 767 g1153.t1 2619 g50281.t14.692839925 0.711873688 −4.12247 0.378768 −5.08558 0.003347 768 g5373.t12620 g9561.t1 5.888238765 0.935705267 −4.23339 0.376965 −5.08426 0.00335769 g7390.t1 2621 g7172.t1 7.350351967 1.129748696 −5.65043 0.372725−5.08115 0.00336 770 g10732.t1 2622 g42561 0 2.447676888 2.516430.360788 5.072408 0.003395 771 g10093.t1 2623 g9511.t1 4.2969649967.412793324 2.89405 0.344563 5.060539 0.003447 772 g10839.t1 2624 g983716.8729034 0 −6.33439 0.32456 −5.04593 0.003498 773 g10191.t1 2625g11148.t1 6.023102414 1.409452743 −5.2232 0.315504 −5.03933 0.00352 774g3013.t1 2626 g8294.t1 5.470261921 0 −5.44413 0.305958 −5.03237 0.003541775 g7841.t1 2627 g10495.t1 4.614472875 0.757799789 −3.27057 0.251911−4.9931 0.003718 776 g21528.t1 2512 g10587.t1 K01885: EARS, 3.9112321080.261005346 −4.64558 0.221495 −4.97108 0.003811 gltx 777 g9138.t1 2628g6473.t1 4.198675014 0.770128672 −3.1553 0.143776 −4.91509 0.004074 778g4873.t1 2629 g4492.t1 5.713341579 2.816941964 −3.86408 0.10615 −4.888120.004228 779 g7446.t1 2630 g6892.t1 7.48417852 1.943606982 −5.038280.095087 −4.88021 0.004261 780 g8021.t1 2631 g8248.t1 4.3097936966.49982563 2.314873 0.091858 4.8779 0.004272 781 g100.t1 2632 g2920.t1 02.543445727 2.527428 0.077045 4.867319 0.00432 782 g1180.t1 2633 g337.t16.10473465 0.378277281 −5.07738 0.074749 −4.86568 0.004327 783 g14694.t12634 g6409.t1 9.825681474 1.554052399 −6.86013 0.073057 −4.864470.004331 784 g6706.t1 2521 g4310.t1 7.446014886 3.740313179 −3.308610.057195 −4.85316 0.004389 785 g14790.t1 2635 g5147.t1 1.6860075486.647954724 6.114271 0.049884 4.847953 0.004415 786 g8676.t1 2636g10948.t1 3.991647742 0.809756341 −3.46435 0.037282 −4.83898 0.004447787 g4402.t1 2637 g2161.t1 0 4.419507408 4.457627 0.01987 4.8266050.004499 788 g1963.t1 2638 g6215.t1 6.923009485 1.722062181 −5.096660.004896 −4.81597 0.004554 789 g132.t1 2639 g5829.t1 0 8.1476235626.459604 −0.00779 4.806976 0.004594 790 g11512.t1 2640 g4219.t16.309781587 3.849786723 −2.31991 −0.01622 −4.80101 0.004625 791g10280.t1 2641 g10638.t1 0 6.450195037 4.96722 −0.02376 4.795666 0.00466792 g796.t1 2642 g8160.t1 0.721237136 8.130353179 6.315026 −0.031644.790094 0.004696 793 g15000.t1 2643 g3110.t1 K09658: DPM2 5.4691564610.297925928 −5.04598 −0.03768 −4.78582 0.004716 794 g7638.t1 2644g7605.t1 0 5.862148582 5.707939 −0.06956 4.763314 0.004863 795 g11518.t12645 g4213.t1 5.935642711 3.230236428 −2.8374 −0.10943 −4.73525 0.005047796 g85.t1 2646 g2767.t1 5.850559685 1.199045091 −4.36726 −0.11833−4.729 0.00509 797 g489.t1 2647 g5491.t1 K05857: PLCD 5.7899254930.871860339 −7.01828 −0.12739 −4.72264 0.005126 798 g8243.t1 2648g10036.t1 4.646855045 0.330447252 −5.92622 −0.1483 −4.70798 0.005219 800g4842.t1 2650 g4453.t1 K13120: 5.230120767 1.098104153 −4.19885 −0.16955−4.6931 0.005312 FAM32A 799 g10374.t1 2649 g10541.t1 K15505: RAD5 02.933131491 3.290135 −0.16944 4.69318 0.005312 801 g10174.t1 2651g8450.t1 K11557: SPC24 1.118361424 6.021652199 4.83424 −0.17145 4.6917750.005318 803 g3427.t1 2653 g4718.t1 K12854: 7.533706795 2.002833589−5.05292 −0.19244 −4.67711 0.005407 SNRNP200, BRR2 802 g1849.t1 2652g1896.t1 K00938: 8.103944385 3.578287021 −4.08273 −0.18889 −4.679590.005407 E2.7.4.2, mvaK2 804 g19694.t1 2654 g7947.t1 K02142: 4.7244789140.648456799 −3.72185 −0.21394 −4.66212 0.005504 ATPeFJ, ATP18 805g6500.t1 2655 g2087.t1 K11548: NUF2, 4.167333488 2.020784202 −2.43559−0.21784 −4.6594 0.005514 CDCA1 808 g11718.t1 2657 g2320.t1 6.9553328760.580666117 −6.38818 −0.22369 −4.65532 0.005525 807 g2706.t1 2513g8366.t1 K11649: 5.407509356 2.809100574 −2.35658 −0.22257 −4.656110.005525 SMARCC 806 g3663.t1 2656 g656.t1 K00632: 6.1076489994.097390482 −2.23548 −0.2214 −4.65692 0.005525 E2.3.1.16, fadA 809g4795.t1 2658 g3691.t1 2.814605061 5.263030629 2.68504 −0.23653 4.6463880.005581 810 g9159.t1 2659 g6490.t1 12.37001214 1.906016093 −7.95994−0.23905 −4.64464 0.005585 812 g7897.t1 2661 g8633.t1 K12191:6.149239272 3.374272912 −2.55359 −0.24971 −4.63722 0.005633 CHMP2A 811g4381.t1 2660 g2138.t1 K14846: RPF1 4.661983349 2.229412642 −2.2735−0.24919 −4.63759 0.005633 813 g15305.t1 2662 g10450.t1 K01915: gluA,1.326818728 5.191947 3.218252 −0.25601 4.632846 0.005659 GLUL 814g12732.t1 2663 g5706.t1 0 5.175711473 5.284348 −0.27649 4.6186380.005755 815 g9791.t1 2664 g893.t1 4.682251788 0.457571639 −3.67907−0.28594 −4.61209 0.0058 816 g14760.t1 2665 g9241.t1 2.8164968915.901553526 3.155387 −0.2866 4.611627 0.0058 817 g5187.t1 2666 g3776.t1K01277: 5.729836476 1.938854906 −4.27181 −0.29258 −4.60749 0.005825E3.4.14.4, DPP3 818 g7634.t1 2667 g7610.t1 K10773: NTH 6.0817787453.751441415 −2.52835 −0.29951 −4.60269 0.005855 819 g13477.t1 2668g8720.t1 K10295: FBXO9 5.178686522 0.847940328 −3.32137 −0.32592−4.58442 0.006017 820 g12592.t1 2669 g2931.t1 6.934534554 2.5557465−4.96282 −0.34887 −4.56858 0.006156 821 g10987.t1 2670 g5653.t1 05.505094032 4.420758 −0.36167 4.559767 0.006238 822 g12590.t1 2671g2934.t1 6.223414116 2.080339763 −3.66131 −0.36679 −4.55624 0.006268 823g10222.t1 2672 g11207.t1 4.643453596 0.715469044 −4.2781 −0.38183−4.54589 0.006357 825 g3983.t1 2674 g7058.t1 K01613: psd, 5.4516657521.425755818 −3.75003 −0.3861 −4.54296 0.006362 PISD 824 g11510.t1 2673g4221.t1 4.286646074 0.732571213 −3.30399 −0.38598 −4.54303 0.006362 826g9393.t1 2675 g3641.t1 8.751164208 1.858084528 −5.0271 −0.39476 −4.5370.006412 827 g9881.t1 2676 g11623.t1 0 5.108233831 5.231226 −0.398384.534514 0.006433 828 g13221.t1 2677 g672.t1 0 2.220629054 2.40642−0.40728 4.528399 0.00648 829 g3561.t1 2678 g3326.t1 4.7334008180.999936795 −4.02216 −0.42399 −4.51694 0.006569 830 g8670.t1 2679g10955.t1 4.749528223 0.956968472 −3.3446 −0.42698 −4.51489 0.006581 831g708.t1 2680 g9946.t1 0.954625619 7.666771535 4.889688 −0.44251 4.5042480.006673 832 g11009.t1 2681 g5663.t1 K11121: SIR2 0 4.462106061 3.362316−0.44719 4.501046 0.006692 833 g7419.t1 2682 g7204.t1 K13754: 6.276106620.798417819 −5.95745 −0.45635 −4.49478 0.006748 SLC24A6, NCKX6 835g3224.t1 2684 g6091.t1 3.344134063 0.745638707 −2.59361 −0.48058−4.47822 0.006877 834 g12947.t1 2683 g9800.t1 0 2.039008683 2.449259−0.48038 4.478357 0.006877 836 g6094.t1 2685 g7354.t1 6.098535871.272304701 −4.60015 −0.49143 −4.47081 0.006946 837 g7427.t1 2686g7212.t1 K01549: TIM11, 5.301910749 3.138905614 −2.18675 −0.49273−4.46993 0.006946 ATP21 838 g6135.t1 2687 g7308.t1 K03844: ALG114.695297001 0 −3.96218 −0.49789 −4.46641 0.006961 839 g5057.t1 2688g8325.t1 K00326: 5.161405198 0.441358118 −4.38384 −0.50196 −4.463640.006974 E1.6.2.2 840 g3875.t1 2689 g4019.t1 1.368553327 4.076971192.537012 −0.50227 4.463427 0.006974 841 g21658.t1 2690 g4834.t16.709472946 3.744824974 −2.67465 −0.52217 −4.44987 0.007097 842 g7438.t12691 g7223.t1 4.971359373 0.658532988 −3.53015 −0.52453 −4.448270.007102 843 g7605.t1 2692 g7631.t1 K06942: K06942 4.937065903 0−4.46853 −0.54372 −4.43522 0.007224 844 g6721.t1 2693 g4326.t11.642040135 5.483246572 3.820601 −0.54429 4.434824 0.007224 845 g7857.t12694 g10514.t1 0 4.218558155 3.368666 −0.54552 4.433987 0.007229 846g3614.t1 2695 g588.t1 K12604: 6.72026689 0.531333536 −5.80897 −0.5699−4.41744 0.007352 CNOT1, NOT1 847 g11968.t1 2696 g7463.t1 0 5.1258106174.200583 −0.57194 4.416052 0.007359 848 g6429.t1 2697 g5353.t15.059361503 1.508836141 −4.45308 −0.57862 −4.41153 0.007396 849g20508.t1 2698 g3950.t1 0 4.196864651 4.108622 −0.58006 4.4105470.007402 850 g7165.t1 2699 g555.t1 3.895318144 0 −4.14265 −0.58148−4.40958 0.007408 851 g4535.t1 2700 g4065.t1 8.36766264 2.386025864−6.90475 −0.60002 −4.39703 0.007531 852 g20378.t1 2701 g3507.t1 07.391829386 7.341373 −0.61198 4.388939 0.007608 853 g8160.t1 2702g11151.t1 7.072684453 0.280401415 −6.23052 −0.6128 −4.38838 0.007609 854g6555.t1 2703 g10091.t1 K00286: 5.981191238 0 −5.84296 −0.61807 −4.384820.007637 E1.5.1.2, proC 855 g5572.t1 2704 g7489.t1 6.09988898410.89359383 4.483809 −0.62462 4.380391 0.00768 856 g2329.t1 2543g9194.t1 7.114801788 3.574070188 −2.75777 −0.63106 −4.37604 0.007723 857g1250.t1 2705 g434.t1 5.533904052 3.185653977 −2.63104 −0.63216 −4.37530.007727 858 g11133.t1 2706 g753.t1 K06972: K06972 4.000597283 0−3.93177 −0.63567 −4.37293 0.007745 859 g490.t1 2536 g5492.t1 K01230:MAN1 4.455711732 0.821736911 −3.64067 −0.66191 −4.35523 0.007924 860g7575.t1 2707 g7666.t1 K11272: MRC1 7.443866007 1.513388401 −5.92967−0.67062 −4.34936 0.007991 861 g6402.t1 2708 g5392.t1 0 5.2885628715.164408 −0.67364 4.347332 0.008003 519 g31.t1 2315 g2840.t1 K02437:gcvH, 7.667805418 2.153109228 −5.17926 −0.68969 −4.33653 0.008113 GCSH862 g11374.t1 2709 g5061.t1 K16803: CKAP5, 0 2.924286464 3.494282−0.6901 4.33625 0.008113 XMAP215 863 g6116.t1 2710 g7333.t1 K02258: 04.831002225 5.170113 −0.7042 4.326775 0.008209 COX11 864 g7600.t1 2711g7636.t1 K17768: 5.478745927 0.350736603 −4.55951 −0.71336 −4.320620.008262 TOM70 865 g7609.t1 2712 g7627.t1 6.110778129 0.897423937−5.14471 −0.71421 −4.32005 0.008264 866 g670.t1 2713 g9895.t15.389860972 3.02046933 −2.23527 −0.72773 −4.31098 0.008362 867 g3288.t12714 g8848.t1 0 4.148359441 4.700775 −0.72891 4.310188 0.008367 868g1739.t1 2715 g9739.t1 K01918: panC 1.723333708 7.241823447 4.71758−0.73179 4.308255 0.008388 869 g2853.t1 2716 g9055.t1 3.6611501170.362821722 −3.21259 −0.73646 −4.30512 0.008418 870 g11104.t1 2717g718.t1 5.331556226 1.94750928 −2.81205 −0.74858 −4.297 0.008489 871g2178.t1 2718 g11917.t1 4.412098474 0 −3.47396 −0.75224 −4.29455 0.00851872 g4449.t1 2719 g6805.t1 7.334855344 0.627760328 −5.29907 −0.7639−4.28674 0.008589 873 g5221.t1 2720 g3709.t1 K01240: URH1 4.3953337470.951987955 −3.0524 −0.76717 −4.28455 0.008614 874 g2815.t1 2721g9114.t1 K01193: 6.290191463 0.734008502 −6.22448 −0.77307 −4.280610.008657 E3.2.1.26, sacA 875 g2269.t1 2722 g10685.t1 2.5514288280.296780765 −2.07634 −0.77841 −4.27704 0.008695 876 g2163.t1 2723g11902.t1 5.298538589 2.694353324 −2.70682 −0.79002 −4.26927 0.008782877 g3515.t1 2724 g2207.t1 3.347586286 6.450463175 3.82448 −0.799224.263133 0.008844 878 g6074.t1 2725 g3347.t1 6.324042809 2.140747407−6.13606 −0.81393 −4.25332 0.008927 879 g11929.t1 2726 g2071.t16.098181798 2.173954682 −4.47826 −0.81655 −4.25157 0.00894 880 g6915.t12727 g1291.t1 K00505: TYR 6.540932521 1.6914174 −4.77307 −0.81897−4.24996 0.008951 881 g1756.t1 2728 g1207.t1 K15201: 6.7310059782.35645327 −4.64979 −0.83531 −4.23907 0.009074 GTP3C3, TFC4 882 g6770.t12729 g4386.t1 5.731686881 3.30963121 −2.17414 −0.83911 −4.23654 0.009106883 g10376.t1 2730 g10544.t1 K02990: RP-S6, 0 2.158000596 2.42587−0.84519 4.232488 0.00916 MRPS6, rpsF 884 g9812.t1 2731 g10826.t1K01899: LSC1 5.913334166 2.531678954 −3.1414 −0.84671 −4.23148 0.009169885 g9618.t1 2732 g7244.t1 0 2.194869885 2.402679 −0.84832 4.2304060.009172 886 g2442.t1 2733 g6711.t1 K10998: CSM3, 6.56163386 2.193043465−3.49995 −0.85623 −4.22514 0.009214 SWI3 887 g17691.t1 2734 g559.t15.586773168 0.314001411 −5.55798 −0.86027 −4.22245 0.009226 889g10183.t1 2736 g11138.t1 K17878: NNT1 4.422235435 0.712887218 −4.88085−0.86671 −4.21817 0.009265 888 g7714.t1 2735 g3081.t1 K01070: frmB,4.789610997 0.611123391 −3.75978 −0.86634 −4.21842 0.009265 ESD, fghA890 g2359.t1 2737 g9253.t1 8.893941672 1.141019105 −7.87059 −0.88299−4.20736 0.009375 891 g4991.t1 2738 g8961.t1 K15901: CGI121, 5.4587783571.709043647 −3.91338 −0.8871 −4.20463 0.009395 TPRKB 892 g106.t1 2739g2927.t1 4.560793659 1.101158731 −3.40776 −0.88917 −4.20326 0.009404 893g7472.t1 2740 g6864.t1 K10839: RAD23, 6.506527453 2.213804236 −4.55459−0.90647 −4.19178 0.00955 HR23 894 g4849.t1 2741 g4462.t1 6.0180499111.275657111 −4.20948 −0.91395 −4.18682 0.009596 895 g4668.t1 2742g10566.t1 K01312: PRSS 9.271875621 0.352165126 −7.40328 −0.918 −4.184140.009626 896 g9585.t1 2743 g6636.t1 K06675: SMC4 0 2.683347982 2.354425−0.92977 4.176344 0.00973 897 g2963.t1 2744 g5934.t1 4.3753286820.740211298 −2.9098 −0.93127 −4.17535 0.00974 898 g7232.t1 2745g10757.t1 K09313: CUTL 8.116353121 2.395376228 −4.44254 −0.9342 −4.173410.009764 899 g19769.t1 2746 g11692.t1 4.972241584 0.686771667 −4.62795−0.94048 −4.16926 0.009812 900 g7022.t1 2747 g6357.t1 0 4.4691804656.919872 −0.94401 4.166923 0.009837 901 g9259.t1 2748 g10437.t16.69953931 2.882217215 −4.44428 −0.94674 −4.16512 0.009859 902 g12328.t12749 g7434.t1 K01710: 3.685729613 0 −2.81719 −0.9494 −4.16336 0.009881E4.2.1.46, rfbB, rffG 903 g2849.t1 2750 g9051.t1 7.214498977 3.486426657−4.11858 −0.95426 −4.16014 0.009921 904 g17779.t1 2751 g662.t14.282054458 1.24041635 −3.15204 −0.95549 −4.15933 0.009928 905 g8550.t12752 g5428.t1 K08838: 5.000505255 0.925832893 −3.77285 −0.9583 −4.157470.009945 STK24_25_ MST4 906 g10940.t1 2753 g1025.t1 K00100: E1.1.1.-4.956194307 1.938081563 −3.28418 −0.95965 −4.15658 0.009953 907g11117.t1 2754 g735.t1 5.648961974 0 −5.52502 −0.96997 −4.14977 0.010045562 g1904.t1 2359 g5010.t1 K16261: YAT 2.226821689 8.926092537 4.673774−0.97066 4.149315 0.010046 908 g3804.t1 2755 g8748.t1 5.7932517621.081386438 −4.42774 −0.97346 −4.14747 0.01007 909 g3244.t1 2756g8218.t1 K02838: frr, 0 4.33702816 4.270014 −0.97624 4.14563 0.010094MRRF, RRF 910 g11369.t1 2757 g10756.t1 5.176727673 2.524623108 −3.0042−0.98484 −4.13995 0.010182 611 g7102.t1 2410 g5569.t1 4.1381249762.196818636 −2.56782 −0.98876 −4.13737 0.010206 911 g677.t1 2758g9875.t1 K07140: K07140 5.281680888 0.559439018 −3.98216 −0.99896−4.13064 0.010292 679 g4287.t1 2759 g1939.t1 K00275: pdxH, 4.951932852.335225171 −2.22283 −1.00489 −4.12674 0.010332 PNPO 912 g7511.t1 2760g10316.t1 K08286: 6.009945831 1.511594622 −3.89684 −1.00716 −4.125240.010351 E2.7.11.- 913 g1830.t1 2761 g1716.t1 7.072977042 1.544496353−5.26083 −1.01212 −4.12197 0.01038 914 g6552.t1 2762 g10088.t1 K14572:MDN1, 4.349948417 6.391579804 2.423474 −1.01251 4.121713 0.01038 REA1915 g74.t1 2763 g917.t1 K00480: 5.955742918 1.714884516 −3.78652−1.01346 −4.12109 0.010382 E1.14.13.1 916 g5429.t1 2764 g3125.t14.987582363 1.729090589 −4.13011 −1.0233 −4.11461 0.010466 917 g8498.t12765 g3370.t1 5.820660636 0.413151614 −5.47293 −1.02797 −4.111540.010506 918 g7844.t1 2766 g10497.t1 5.848243945 1.578952778 −4.16193−1.03098 −4.10956 0.010524 919 g5407.t1 2767 g8613.t1 0 5.5347330824.711339 −1.03102 4.109529 0.010524 921 g4889.t1 2769 g4523.t1 K14209:5.82364098 0.611123391 −5.50761 −1.03508 −4.10686 0.010547 SLC36A, PAT920 g2118.t1 2768 g2464.t1 K01560: E3.8.1.2 3.940755827 0.663970885−2.81812 −1.03464 −4.10715 0.010547 922 g4577.t1 2770 g4105.t12.560658097 5.985251291 3.589267 −1.03779 4.105077 0.010566 923 g6091.t12771 g7357.t1 K12193: VPS24, 2.859023838 6.502695672 3.091915 −1.040934.103011 0.010586 CHMP3 924 g4043.t1 2772 g3220.t1 5.0964647481.443935828 −4.5113 −1.05361 −4.09468 0.010703 925 g10590.t1 2773g7033.t1 K01190: lacZ 0 2.243268623 3.095296 −1.06313 4.088427 0.010784926 g11987.t1 2774 g2441.t1 K15172: 6.055881291 2.362058349 −3.85574−1.06897 −4.0846 0.010834 SUPT5H, SPT5 927 g7118.t1 2775 g5583.t1K06670: SCC1, 7.656991383 0.390883076 −7.66832 −1.07595 −4.080020.010905 MCD1, RAD21 928 g9841.t1 2776 g9760.t1 8.545788709 2.867657374−4.92548 −1.082 −4.07604 0.010958 929 g10869.t1 2777 g134.t1 04.541052906 5.755119 −1.09914 4.06481 0.011149 930 g8799.t1 2778g9975.t1 4.851135285 2.848977141 −2.03413 −1.10105 −4.06356 0.011158 931g3513.t1 2779 g2205.t1 K12041: 4.628300692 7.602958834 4.626855 −1.104734.061149 0.011189 SLC9A6_7, NHE6_7 932 g4464.t1 2780 g6823.t1 K00111:glpA, 4.913318358 1.479604123 −3.34305 −1.1065 −4.05999 0.011196 glpD933 g912.t1 2781 g9350.t1 6.681560463 1.806751763 −4.31686 −1.1196−4.05142 0.011342 934 g6047.t1 2482 g264.t1 5.833182512 0.677369437−5.13698 −1.12643 −4.04694 0.011405 935 g8273.t1 2782 g9995.t15.609052156 1.060347821 −4.34904 −1.14015 −4.03798 0.011561 936 g8132.t12783 g7944.t1 K14526: POP7, 5.431104442 0.674479047 −4.05357 −1.14688−4.03357 0.011602 RPP2 937 g8077.t1 2540 g7846.t1 6.9245798293.179764724 −3.71311 −1.15782 −4.02643 0.011726 938 g10164.t1 2784g6116.t1 6.523454108 2.07702255 −4.71124 −1.17646 −4.01427 0.011932 940g8187.t1 2785 g7995.t1 K03325: 8.04995065 0.87529095 −5.79877 −1.18683−4.0075 0.012033 TC.ACR3 939 g4598.t1 2528 g6014.t1 3.9858359118.056156653 3.69429 −1.18652 4.007708 0.012033 941 g10685.t1 2786g8531.t1 4.755054229 0.597731661 −5.22216 −1.18923 −4.00594 0.012049 942g4368.t1 2787 g3790.t1 5.47962036 0.600445772 −5.6468 −1.19165 −4.004360.012073 944 g5574.t1 2789 g7491.t1 K11370: AHC1 7.953609684 0 −8.04647−1.19703 −4.00086 0.012107 943 g10154.t1 2788 g8466.t1 K03661:2.459230154 8.648411182 5.524738 −1.19676 4.001038 0.012107 ATPeV0B,ATP6F 945 g6618.t1 2790 g11273.t1 K14333: DHBD 8.223627165 4.489647578−3.74758 −1.20103 −3.99825 0.012152 946 g4717.t1 2791 g2039.t16.556761484 0.832520653 −5.79326 −1.2067 −3.99456 0.012204 947 g3409.t12792 g6220.t1 6.131735085 2.932298929 −4.4842 −1.21334 −3.99024 0.012261948 g11995.t1 2793 g2451.t1 4.464464914 0.151188629 −4.14283 −1.21373−3.98998 0.012261 949 g2327.t1 2794 g9192.t1 4.697725891 3.031852784−2.51819 −1.22384 −3.98341 0.01238 950 g4993.t1 2795 g8964.t15.277688941 1.187953513 −4.53745 −1.225 −3.98265 0.012388 951 g9979.t12796 g9685.t1 K15148: MED7 0 5.949359522 6.520548 −1.22659 3.9816180.012402 952 g6193.t1 2797 g11718.t1 6.836216759 0.250673031 −7.32329−1.23434 −3.97658 0.012461 953 g4069.t1 2798 g3263.t1 4.4379177771.954717425 −2.12779 −1.24126 −3.97208 0.012532 954 g10250.t1 2799g3606.t1 12.0823581 5.349202675 −5.14517 −1.24396 −3.97033 0.012561 955g5983.t1 2800 g11682.t1 5.452835216 1.46241328 −3.94481 −1.24535−3.96942 0.012564 957 g11115.t1 2802 g733.t1 6.202864972 1.546483629−4.74294 −1.24702 −3.96834 0.012572 956 g3228.t1 2801 g6074.t14.204057944 1.75745979 −2.38792 −1.24691 −3.96841 0.012572 958 g9407.t12803 g3620.t1 4.931825845 2.242713995 −2.80653 −1.2614 −3.959 0.012715959 g1828.t1 2804 g1714.t1 K13535: CLD1 4.463119082 0.759418996 −4.44127−1.27477 −3.95032 0.012862 960 g3944.t1 2805 g3947.t1 5.535649157 0−5.19232 −1.288 −3.94174 0.012985 961 g7851.t1 2806 g10505.t15.044625434 2.009449375 −2.88495 −1.28967 −3.94066 0.013001 962g18788.t1 2807 g387.t1 6.532520126 0 −5.41093 −1.29136 −3.93956 0.013009963 g9384.t1 2808 g3650.t1 K02210: MCM7, 6.91078027 1.571021615 −4.64794−1.29234 −3.93894 0.013015 CDC47 964 g1127.t1 2809 g226.t1 K13210: FUBP7.124489061 2.229618353 −5.13781 −1.29958 −3.93424 0.013094 965 g96.t12810 g2917.t1 0 5.492351766 4.171895 −1.30404 3.931351 0.013134 966g6648.t1 2811 g10192.t1 K12868: SYF2 0 3.516802163 3.256136 −1.306083.930031 0.013156 967 g1350.t1 2812 g7381.t1 0 3.889064314 4.850634−1.30889 3.928212 0.013188 968 g13893.t1 2813 g6198.t1 K07034: K070346.848687422 0 −6.40524 −1.31197 −3.92621 0.013224 969 g4507.t1 2814g10812.t1 3.840346233 0.671708995 −3.61124 −1.31998 −3.92103 0.013315970 g3241.t1 2815 g8215.t1 0 5.467296488 6.060068 −1.32773 3.9160220.013403 971 g11754.t1 2816 g9856.t1 K01779: 5.221579117 2.774475816−2.73909 −1.33008 −3.9145 0.013416 E5.1.1.13 972 g1351.t1 2817 g6327.t10 1.545461152 2.309288 −1.34311 3.906078 0.013561 973 g2037.t1 2818g2568.t1 K12659: ARG56 0 2.389962015 2.943914 −1.34345 3.905856 0.013561974 g1683.t1 2819 g4660.t1 K10625: UBR1 3.398274676 0 −4.674 −1.35076−3.90114 0.013653 975 g12749.t1 2820 g12137.t1 0 4.230324352 4.826237−1.35244 3.900048 0.013662 976 g9482.t1 2821 g5768.t1 6.717657461.451437878 −4.59504 −1.36048 −3.89485 0.013771 977 g11380.t1 2822g5068.t1 0 7.45098535 7.483026 −1.3621 3.893807 0.013774 978 g6127.t12823 g7319.t1 K07213: ATOX1, 11.50816411 4.935645484 −6.72817 −1.37221−3.88728 0.013876 ATX1, copZ 979 g270.t1 2824 g7700.t1 6.2486190312.885761626 −3.92892 −1.37418 −3.88601 0.013881 980 g6423.t1 2825g5361.t1 3.403273853 6.221604639 2.695089 −1.38022 3.882118 0.013943 981g10729.t1 2826 g2908.t1 K03448: FEN2, 0 3.964745867 3.303213 −1.385283.878855 0.014 LIZ1 982 g3774.t1 2827 g6851.t1 0 3.457188398 2.664168−1.38842 3.876826 0.01404 983 g8680.t1 2828 g10944.t1 K13621: BTA1 05.217325652 5.065179 −1.39706 3.871256 0.014155 985 g11533.t1 2830g4194.t1 K00928: lysC 8.670529213 3.613657545 −5.20151 −1.40566 −3.865710.014246 984 g2060.t1 2829 g2537.t1 4.647437267 0 −3.66136 −1.40528−3.86596 0.014246 987 g6588.t1 2832 g11117.t1 5.93851127 1.623174665−4.60564 −1.40762 −3.86446 0.014246 986 g9187.t1 2831 g6519.t10.369867578 6.089917916 7.049988 −1.40678 3.864993 0.014246 988 g2854.t12833 g4992.t1 3.667696129 8.241283975 5.523058 −1.40977 3.8630720.014268 989 g173.t1 2834 g5800.t1 K07119: K07119 9.3703401414.321377749 −3.96851 −1.41225 −3.86147 0.014299 545 g10561.t1 2342g1546.t1 0 4.450650367 6.044056 −1.42629 3.852432 0.014477 990 g5941.t12835 g2881.t1 0 2.254791406 2.038211 −1.4329 3.848179 0.01457 991g2978.t1 2836 g8309.t1 0 10.62344924 7.901472 −1.43469 3.847032 0.014582992 g1958.t1 2837 g6209.t1 9.099456694 1.119311238 −6.95438 −1.43536−3.8466 0.014585 993 g12003.t1 2838 g10167.t1 4.021343839 0.753679573−3.29178 −1.44029 −3.84343 0.014654 994 g18673.t1 2839 g8118.t11.798228538 5.146898574 3.430541 −1.44724 3.838958 0.014756 996g11700.t1 2841 g6614.t1 K03860: PIGQ, 4.969629765 0.352559564 −4.46723−1.45227 −3.83573 0.014818 GPU 997 g5957.t1 2842 g6229.t1 K01056: PTH1,0 1.976704664 2.01366 −1.45267 3.835472 0.014818 pth, spoVC 995g21700.t1 2840 g5543.t1 3.167921414 5.319048056 2.74517 −1.452153.835802 0.014818 998 g8304.t1 2843 g5092.t1 K10253: K10253 4.6210449930.255280379 −3.70757 −1.4678 −3.82575 0.015036 1000 g697.t1 2845g9928.t1 K03941: 5.799554424 1.181054579 −4.15809 −1.4692 −3.824850.015042 NDUFS8 999 g10287.t1 2844 g36.t1 K15444: TRM9 0 5.8743059575.783803 −1.46917 3.824872 0.015042 1001 g2303.t1 2846 g10723.t1 K07441:ALG14 5.074009843 1.567191477 −3.7165 −1.47258 −3.82268 0.015079 1002g6384.t1 2847 g759.t1 6.12726441 3.083653978 −2.87756 −1.48007 −3.817870.015176 1003 g7586.t1 2848 g7651.t1 5.043611275 1.963825039 −3.6841−1.49291 −3.80963 0.015336 1004 g8534.t1 2849 g6285.t1 0 6.2470107545.020519 −1.52096 3.791656 0.015745 1005 g5408.t1 2850 g8612.t1 K00276:AOC3, 0 8.151281431 5.76651 −1.52222 3.790847 0.015749 AOC2, tynA 1006g8194.t1 2851 g8514.t1 6.303747883 2.955946512 −2.77841 −1.52803−3.78712 0.015822 1007 g13118.t1 2852 g7773.t1 0 2.046350551 2.429844−1.5376 3.781003 0.01595 1008 g9153.t1 2853 g6485.t1 K18716: NUP42,6.170706947 3.061140417 −4.53758 −1.53902 −3.78009 0.015957 RIP1 1009g6545.t1 2854 g10082.t1 K03885: ndh 0 3.860530568 3.48447 −1.545763.775781 0.016064 1010 g7749.t1 2855 g7099.t1 K01512: acyP 1.4058198985.724724114 3.992675 −1.56158 3.765662 0.01626 1011 g19631.t1 2856g6634.t1 2.571565788 0.506732919 −2.42296 −1.56584 −3.76294 0.0163071012 g522.t1 2857 g889.t1 10.81615793 0 −8.03958 −1.5726 −3.758610.016414 1013 g3484.t1 2858 g2151.t1 0 3.773241919 4.603707 −1.573853.757817 0.016422 1014 g12598.t1 2859 g12.t1 5.489807798 2.727386827−2.67853 −1.57834 −3.75495 0.016483 1016 g2711.t1 2861 g8361.t1 K07195:4.061048103 0.82017382 −4.30659 −1.58513 −3.75061 0.016586 EXOC7, EXO701015 g579.t1 2860 g3880.t1 K14826: FPR3_4 4.281193383 0.923209684−3.22546 −1.58489 −3.75076 0.016586 1017 g5304.t1 2862 g2266.t11.064282379 6.276337463 4.132421 −1.58843 3.748508 0.01663 1018g15818.t1 2863 g5620.t1 5.095758915 1.04393275 −3.79971 −1.60492−3.73798 0.016879 1019 g11541.t1 2864 g4185.t1 K15710: SHPRH 9.3377178583.868672254 −4.98764 −1.60709 −3.73659 0.016905 1020 g5073.t1 2865g8342.t1 K08008: NOX, 0 3.029525217 4.770622 −1.60735 3.73643 0.016905GP91 1022 g6955.t1 2867 g6434.t1 K14860: TMA16 5.89989351 1.267905318−6.51374 −1.61151 −3.73378 0.016916 1021 g6611.t1 2866 g10146.t19.37786699 5.898480598 −4.99071 −1.61123 −3.73396 0.016916 1023g11689.t1 2868 g10851.t1 K10405: KIFC1 3.582191481 0.519463263 −3.48082−1.62299 −3.72646 0.017089 1024 g4428.t1 2869 g6761.t1 7.5155047052.722287062 −5.41187 −1.62797 −3.72328 0.017144 1025 g3928.t1 2870g3964.t1 7.606070252 2.558264062 −4.77608 −1.64316 −3.7136 0.017342 1028g4373.t1 2873 g2130.t1 K13501: TRP1 5.255678294 0.925732567 −4.57859−1.64785 −3.71061 0.017346 1027 g10552.t1 2872 g6698.t1 0 2.639604192.31192 −1.64604 3.711768 0.017346 1026 g4264.t1 2871 g1718.t1 06.178156431 4.998374 −1.64578 3.711931 0.017346 1029 g7551.t1 2874g7255.t1 K14640: 2.536552173 0 −2.40333 −1.65666 −3.705 0.017474 SLC20A,PIT 1030 g73.t1 2875 g914.t1 4.346084349 0.493988199 −4.09124 −1.66098−3.70226 0.017537 1031 g10225.t1 2876 g11203.t1 9.413047495 0.613538354−6.24471 −1.66287 −3.70106 0.017554 1032 g5522.t1 2877 g1649.t1 K11699:RDR, 5.864561275 1.938062923 −3.04363 −1.66588 −3.69914 0.017592 RDRP1033 g7042.t1 2878 g6333.t1 4.730082423 1.654400295 −2.98841 −1.67296−3.69463 0.017699 1034 g4256.t1 2879 g1726.t1 K11254: H4 5.3925556433.344095815 −2.53578 −1.68387 −3.68769 0.017848 1036 g1108.t1 2881g4055.t1 K11131: DKC1, 4.027072029 1.511031928 −2.40023 −1.68571−3.68653 0.017848 NOLA4, CBF5 1035 g8681.t1 2880 g10943.t1 K00237: SDHD,0 8.70058704 7.017271 −1.68454 3.687266 0.017848 SDH4 1037 g11120.t12520 g739.t1 K11309: 5.304552729 8.043114244 3.98187 −1.68842 3.6848010.017891 RTT109, KAT11 1038 g10725.t1 2882 g4263.t1 K01495: GCH1,7.095909192 1.607176292 −5.94728 −1.69053 −3.68346 0.017922 folE 1039g9660.t1 2883 g4874.t1 0.457027413 5.574517372 4.436765 −1.695633.680219 0.018002 1040 g8820.t1 2884 g3030.t1 5.372767428 0.370292524−4.05667 −1.6974 −3.67909 0.018007 1041 g4065.t1 2885 g3253.t1 K03362:3.768457818 1.950585648 −2.47011 −1.69787 −3.67879 0.018007 FBXW1_11,BTRC, beta-TRCP 1042 g5448.t1 2886 g3163.t1 5.226224828 3.242059589−2.42483 −1.70473 −3.67444 0.018122 1043 g7588.t1 2887 g7649.t16.811316171 1.76280266 −3.78597 −1.7088 −3.67185 0.018192 1044 g3582.t12888 g5074.t1 K00293: LYS9 3.263233452 1.316734534 −2.09676 −1.71032−3.67089 0.018202 1045 g6422.t1 2889 g5364.t1 2.147147382 5.1643037022.861711 −1.71391 3.668603 0.018254 483 g10693.t1 2485 g8538.t15.662368091 3.168076577 −4.05295 −1.71839 −3.66576 0.018333 1046g6032.t1 2890 g11214.t1 8.820793561 3.54374382 −7.9404 −1.72085 −3.66420.018372 1047 g6561.t1 2891 g10097.t1 5.654687421 2.820296417 −2.65197−1.7243 −3.66201 0.018411 1048 g2191.t1 2892 g11582.t1 K03352: APC54.67408688 1.782772866 −3.29686 −1.72886 −3.65912 0.018482 1049 g8669.t12893 g10956.t1 4.818547725 2.715853793 −3.19505 −1.73268 −3.656690.018539 1050 g5585.t1 2894 g7506.t1 K14300: NUP133 5.4502169322.124950228 −3.36335 −1.73378 −3.656 0.018551 1051 g6577.t1 2895g2327.t1 8.791267353 3.370950467 −4.38699 −1.73587 −3.65467 0.0185731052 g4912.t1 2896 g4547.t1 0 4.635965828 4.676103 −1.73742 3.6536820.018585 1053 g5600.t1 2897 g7522.t1 K17787: AIM5 0 3.93663278 3.907389−1.74421 3.649379 0.018705 1054 g59.t1 2898 g2750.t1 K09529: 05.496293536 5.677194 −1.75422 3.643028 0.018876 DNAJC9 1055 g2459.t12899 g67311.t1 2.631378842 1.157983737 −2.10785 −1.75717 −3.641160.018906 1056 g3841.t1 2900 g2574.t1 5.178143897 2.175433875 −2.89829−1.7677 −3.63449 0.019072 1058 g10928.t1 2902 g11230.t1 K09291: TPR2.438636081 5.135322312 2.167023 −1.76965 3.633253 0.019092 1057g4517.t1 2901 g10822.t1 0 5.512328424 5.554663 −1.7695 3.633348 0.0190921059 g5642.t1 2903 g9240.t1 10.22312916 5.571257573 −3.6137 −1.77777−3.62811 0.01922 1060 g5649.t1 2904 g1103.t1 4.544636216 0.801147961−4.17727 −1.77847 −3.62766 0.019225 1061 g11163.t1 2905 g4845.t1 K00838:ARO8 0.832183706 5.305901271 4.234911 −1.78279 3.624925 0.019305 1062g5464.t1 2906 g8437.t1 K01487: 4.270772945 0.22548607 −4.11742 −1.79064−3.61996 0.019439 E3.5.4.3, guaD 1063 g6448.t1 2907 g5337.t1 0.7049968324.000286115 4.304908 −1.79379 3.617966 0.019484 1064 g546.t1 2908g5611.t1 5.264731099 1.369172577 −3.2191 −1.79682 −3.61605 0.019538 1065g970.t1 2909 g8041.t1 5.740601251 1.557405801 −3.67053 −1.80007 −3.613990.019576 1066 g196.t1 2910 g5304.t1 4.777372465 1.654308781 −2.76658−1.80086 −3.61349 0.019583 1067 g1283.t1 2911 g473.t1 0 3.8426565866.802298 −1.80742 3.609337 0.019702 1068 g12044.t1 2912 g803.t15.498118982 3.142019176 −2.65907 −1.80959 −3.60797 0.019728 1069g9074.t1 2913 g8565.t1 0 5.223284374 5.133706 −1.81049 3.607396 0.0197371070 g10056.t1 2914 g2782.t1 K05351: 7.25059785 2.52330656 −4.70108−1.82053 −3.60105 0.019899 E1.1.1.9 1071 g12237.t1 2915 g11133.t1K17878: NNT1 4.149357354 1.472587157 −3.10449 −1.82085 −3.60084 0.0198991072 g4465.t1 2916 g6824.t1 5.086524971 0.645587044 −4.07666 −1.82154−3.60041 0.019901 1073 g1040.t1 2917 g8111.t1 0 5.890637103 5.870779−1.8259 3.597655 0.019975 1074 g8432.t1 2918 g2491.t1 0 5.000019544.190313 −1.82818 3.596214 0.020014 1075 g9956.t1 2919 g11404.t1 06.541463318 5.35561 −1.83034 3.594846 0.02005 1077 g4593.t1 2921g6010.t1 6.800127858 3.549959281 −2.93876 −1.83506 −3.59186 0.0201321076 g449.t1 2920 g8027.t1 2.548177204 6.213381276 3.478537 −1.835043.591878 0.020132 1078 g15695.t1 2922 g10590.t1 0 7.173454513 6.185129−1.83708 3.590587 0.020145 1079 g7238.t1 2923 g10763.t1 6.636516842 0−4.81827 −1.84088 −3.58819 0.020217 1080 g2270.t1 2924 g10687.t1 K01551:arsA, 1.338776738 5.795884869 4.024342 −1.84369 3.586412 0.020268 ASNA11081 g7667.t1 2925 g7562.t1 K01469: OPLAH, 4.982517875 0.932891826−3.4849 −1.845 −3.58558 0.020287 OXP1, oplAH 1082 g5077.t1 2926 g4465.t1K01193: 0 2.960911198 3.374984 −1.84621 3.584819 0.020303 E3.2.1.26,sacA 1083 g6226.t1 2927 g7123.t1 K12609: CAF120 5.821481969 0.802806449−5.22139 −1.85419 −3.57978 0.020457 1084 g5075.t1 2928 g2985.t1 04.80563983 3.713653 −1.85653 3.578302 0.020488 1085 g13910.t1 2929g8741.t1 3.759982388 0.360268275 −3.12849 −1.87274 −3.56807 0.0208071086 g8085.t1 2930 g78631.t1 7.812628972 1.145353766 −4.97699 −1.87917−3.56401 0.02092 1087 g10423.t1 2931 g8402.t1 K14327: UPF2, 5.3807499710.19444946 −4.70673 −1.88023 −3.56334 0.020927 RENT2 1088 g11332.t1 2932g11641.t1 4.160151798 2.045122287 −2.26209 −1.8804 −3.56323 0.0209271089 g7007.t1 2933 g6374.t1 K12600: SKI3, 0 2.790129292 3.618279−1.88398 3.560979 0.020986 TTC37 1090 g2160.t1 2934 g11899.t12.646205187 0.257249951 −3.58225 −1.88632 −3.5595 0.021018 1091 g3470.t12935 g2763.t1 K00140: mmsA, 6.130826774 0.21865482 −4.84924 −1.88786−3.55853 0.021042 iolA, ALDH6A1 1092 g10929.t1 2936 g11231.t1 K14805:DDX24, 4.672508797 1.17072715 −3.01023 −1.8894 −3.55756 0.021066 MAK51093 g5608.t1 2937 g7532.t1 0.756308574 5.212354025 3.853227 −1.889843.557283 0.021066 1094 g7845.t1 2938 g10498.t1 K03434: PIGL 8.1817374551.583646888 −6.91124 −1.89564 −3.55362 0.021156 1095 g15860.t1 2939g6739.t1 K09831: ERG5 5.065082896 0.529768939 −3.57805 −1.89631 −3.55320.02116 1096 g584.t1 2940 g3874.t1 K01520: dut, 4.447661542 0.440246825−4.18025 −1.89957 −3.55115 0.021224 DUT 1097 g5992.t1 2941 g11691.t1K06276: PDPK1 4.323838023 1.006472653 −3.77529 −1.90915 −3.545110.021424 1098 g9408.t1 2942 g3619.t1 6.248005823 2.598887614 −2.71989−1.90919 −3.54508 0.021424 1099 g12324.t1 2943 g7430.t1 K03936:4.250138533 1.633961537 −2.27784 −1.91946 −3.53861 0.021607 NDUFS3 1100g8165.t1 2944 g7972.t1 0.505090398 5.931877819 3.973947 −1.929823.532082 0.021785 1101 g6804.t1 2945 g4428.t1 K15128: MED6 3.9379247351.226226038 −3.06025 −1.93078 −3.53148 0.021797 1102 g4151.t1 2946g1828.t1 K03327: 5.671937128 3.119497464 −2.69006 −1.93393 −3.52950.021849 TC.MATE, SLC47A, norM, mdtK, dinF 1103 g7170.t1 2947 g560.t15.705181185 2.50956836 −3.52997 −1.93676 −3.52772 0.021905 1104 g8819.t12948 g3028.t1 K09252: 6.425640233 2.167666125 −4.21806 −1.94078 −3.525180.021957 E3.1.1.73 1105 g10490.t1 2949 g1671.t1 0.267350656 5.2894008664.58514 −1.94331 3.523591 0.021995 1106 g10438.t1 2950 g8414.t1 K11090:LA, SSB 4.175176818 0.564083606 −3.119 −1.94491 −3.52258 0.022022 1107g7152.t1 2951 g11953.t1 4.892910278 0 −4.28485 −1.94745 −3.520980.022069 1108 g7945.t1 2952 g9700.t1 K15272: 3.910911941 6.8927088722.844791 −1.94782 3.520755 0.022069 SLC35A1_2_3 1110 g5482.t1 2954g9825.t1 K03544: clpX, 5.959845259 3.962799023 −2.6218 −1.95044 −3.51910.02211 CLPX 1109 g9746.t1 2953 g1027.t1 0 3.49762073 3.171806 −1.950023.519371 0.02211 1111 g7512.t1 2955 g10315.t1 K10268: 5.0361025971.924325269 −2.88696 −1.95351 −3.51717 0.022172 FBXL2_20 1112 g9423.t12956 g10311.t1 K17678: MRH4 5.698279892 0.794188824 −4.53867 −1.95601−3.5156 0.02221 1113 g4358.t1 2957 g427.t1 K15394: ACE1 8.4307678362.590016536 −4.22487 −1.96125 −3.5123 0.022313 1114 g2440.t1 2958g6709.t1 8.194390826 0.959769507 −5.65514 −1.96222 −3.51169 0.0223261115 g7412.t1 2959 g7196.t1 K17786: MOS2 4.719997185 0.149385666−4.56381 −1.96848 −3.50776 0.022424 1116 g7292.t1 2960 g11859.t1 K17267:COPG 5.289893047 1.985649581 −3.35694 −1.96926 −3.50726 0.022424 479g10141.t1 2484 g8477.t1 5.541093332 2.791373031 −2.40723 −1.9695−3.50711 0.022424 1117 g5887.t1 2961 g10973.t1 7.17403047 0.786931333−5.65287 −1.97046 −3.50651 0.022436 1119 g1144.t1 2963 g256.t14.804829552 0.756889395 −4.9479 −1.97225 −3.50539 0.022447 1118 g6530.t12962 g10068.t1 K12345: 6.05975643 0.765101758 −4.56855 −1.97188 −3.505620.022447 SRD5A3 1120 g1388.t1 2964 g3922.t1 K11108: RCL1 0 3.6061046844.172772 −1.97523 3.50351 0.022506 660 g8547.t1 2461 g10270.t1 K02865:4.653519091 0.569101736 −4.25142 −1.97772 −3.50195 0.022536 RP-L10Ae,RPL10A 1121 g1443.t1 2965 g6990.t1 6.353729544 3.715374057 −2.42559−1.97777 −3.50191 0.022536 557 g5845.t1 2354 g1158.t1 K02985: 6.789588023.97973657 −3.61504 −1.98019 −3.50039 0.022571 RP-S3e, RPS3 1122g1775.t1 2966 g1180.t1 2.44192219 5.786705282 3.075249 −1.98055 3.5001630.022571 1123 g5301.t1 2967 g2268.t1 4.832199777 1.450036735 −4.59182−1.9812 −3.49976 0.022576 1124 g5630.t1 2968 g1133.t1 K10808: RRM23.538433491 8.044277291 4.332171 −1.98319 3.498506 0.022613 1125g10024.t1 2969 g8702.t1 0 4.379295342 4.698935 −1.98525 3.4972090.022641 1126 g2219.t1 2970 g2626.t1 5.454955353 0.251432019 −3.8457−1.99306 −3.4923 0.02281 1127 g3982.t1 2971 g7057.t1 K07824: 4.4769392921.319684937 −2.77154 −1.99439 −3.49147 0.02281 E1.14.13.12 1129 g8840.t12973 g1272.t1 3.816201878 6.770081287 3.045058 −1.99951 3.4882480.022869 1128 g9861.t1 2972 g11455.t1 K06101: ASH1L 0 4.6335123564.527713 −1.99917 3.488465 0.022869 1130 g4800.t1 2974 g676.t15.81071258 0.839736228 −3.94597 −2.00606 −3.48413 0.022998 1131g11654.t1 2975 g8005.t1 2.909017487 6.248705968 3.378105 −2.009043.482265 0.023049 1132 g1136.t1 2976 g245.t1 10.59339274 4.772886191−4.68428 −2.01923 −3.47586 0.02327 1133 g7223.t1 2977 g5892.t15.576672157 1.870596878 −3.72025 −2.02093 −3.4748 0.02329 1134 g3646.t12978 g623.t1 6.238451943 1.598186508 −3.95284 −2.02649 −3.4713 0.0233851135 g11372.t1 2979 g5059.t1 0 3.180254596 2.748058 −2.0306 3.4687250.023466 1138 g6590.t1 2982 g11119.t1 4.776549031 0 −3.51612 −2.03519−3.46585 0.023548 1136 g1968.t1 2980 g6227.t1 5.415945903 1.846262242−2.98674 −2.0347 −3.46615 0.023548 1137 g991.t1 2981 g8058.t14.169458418 6.394078234 3.701135 −2.03493 3.46601 0.023548 1139 g14.t12983 g11312.t1 5.71723547 2.200469261 −2.90045 −2.03611 −3.46527 0.023561140 g8611.t1 2984 g3033.t1 3.208304365 6.684869911 4.600843 −2.038083.46403 0.023599 1141 g6942.t1 2985 g6445.t1 K00988: APA1_2 0.1223561874.223472162 3.719099 −2.04026 3.462663 0.023643 1142 g4972.t1 2986g8937.t1 K13953: adhP 1.662757196 5.891631852 4.01311 −2.04335 3.4607250.023699 1143 g11708.t1 2987 g6617.t1 6.393154936 0.574680488 −5.63531−2.05038 −3.45631 0.023866 1144 g6627.t1 2988 g10177.t1 4.492307379 0−4.73854 −2.05245 −3.45502 0.023898 1145 g3793.t1 2989 g2622.t1 K00632:2.683933449 0.762155863 −2.33328 −2.05833 −3.45133 0.024039 E2.3.1.16,fadA 1146 g5362.t1 2990 g9549.t1 5.333486397 1.869084159 −3.81693−2.06267 −3.44861 0.02414 1147 g14458.t1 2991 g213.t1 K03417: prpB5.793822468 0.460510026 −4.53188 −2.06694 −3.44593 0.024224 1148g3972.t1 2992 g7050.t1 K09274: K09274 4.82960772 2.115464547 −2.69328−2.07351 −3.44181 0.024331 1149 g9183.t1 2993 g6515.t1 1.7625733427.079679643 4.155095 −2.07513 3.440795 0.02435 1150 g3346.t1 2994g4782.t1 0 3.996837394 3.371635 −2.07771 3.439177 0.024406 1151g15347.t1 2995 g9963.t1 5.425175011 3.445024571 −3.15188 −2.0797−3.43793 0.024436 1152 g610.t1 2996 g3850.t1 0 2.724738444 4.721844−2.07971 3.437925 0.024436 1153 g5842.t1 2997 g1161.t1 4.5637177326.156540077 2.037263 −2.0869 3.433418 0.024569 1154 g13891.t1 2998g7379.t1 0 5.395995421 4.86386 −2.08715 3.433268 0.024569 1155 g13895.t12999 g3474.t1 K07407: 6.607561086 4.158554252 −2.60137 −2.08937 −3.431870.024609 E3.2.1.22B, galA, rafA 1156 g5991.t1 3000 g11690.t1 K11650:6.177996747 0.576104948 −4.263 −2.08984 −3.43158 0.02461 SMARCD 1157g6045.t1 3001 g11733.t1 2.901234647 8.987765157 5.807638 −2.095483.428044 0.024702 1158 g5636.t1 3002 g1113.t1 K08818: CDC2L 7.1978422081.025911245 −5.25317 −2.10189 −3.42403 0.024838 1159 g7137.t1 2541g530.t1 K09702: K09702 5.111190124 0.46928073 −4.29408 −2.10378 −3.422850.024853 1160 g2933.t1 3003 g5977.t1 6.559889482 1.898194519 −3.99948−2.11649 −3.41489 0.025137 1161 g505.t1 3004 g5519.t1 3.8631295526.615728181 2.44593 −2.12415 3.410093 0.025321 1162 g7769.t1 3005g7721.t1 5.577160458 1.98974677 −3.2893 −2.13007 −3.40639 0.025436 1163g7156.t1 3006 g544.t1 6.758034692 0.550773544 −5.82435 −2.13342 −3.404290.025476 1165 g930.t1 3008 g9329.t1 5.15713035 2.062962464 −2.56378−2.13372 −3.4041 0.025476 1164 g13110.t1 3007 g9758.t1 0 2.270104163.871956 −2.13369 3.404124 0.025476 1166 g586.t1 3009 g3871.t13.781116872 0.130099531 −3.60762 −2.14382 −3.39779 0.025688 577 g1391.t12375 g3917.t1 3.770913064 1.227337296 −2.68731 −2.14399 −3.397680.025688 1168 g10165.t1 3011 g7723.t1 K01455: 5.879458438 2.187241836−3.86391 −2.15334 −3.39184 0.025911 E3.5.1.49 1167 g2887.t1 3010g10878.t1 K00102: 4.602956869 2.179867653 −2.46981 −2.15315 −3.391950.025911 E1.1.2.4. dld 689 g849.t1 2496 g9453.t1 K06997: K069973.120625144 0.692301308 −2.11851 −2.15658 −3.38981 0.025968 1169g7214.t1 3012 g5878.t1 4.495077603 0 −3.33078 −2.16097 −3.38706 0.0260651170 g18895.t1 3013 g5859.t1 K10845: TTDA, 5.98025722 0.117852324−4.59309 −2.16486 −3.38463 0.026138 GTF2H5, TFB5 1171 g8250.t1 3014g10029.t1 4.39864019 7.809600987 3.394989 −2.17214 3.380082 0.0262741172 g2364.t1 3015 g9259.t1 9.213191896 3.489449551 −5.38194 −2.1741−3.37886 0.026289 1173 g560.t1 3016 g7760.t1 K07819, 0 2.5471252152.005488 −2.17957 3.375436 0.026433 B3GALT1 1174 g5544.t1 3017 g11318.t1K01874: MARS, 5.478905924 1.205809707 −3.53649 −2.18062 −3.374780.026451 metG 1175 g2772.t1 3018 g9139.t1 K14840: NOP53, 0 4.5041870563.485223 −2.18408 3.372617 0.026537 GLTSCR2 1176 g5248.t1 3019 g2343.t18.877204443 2.997703245 −4.70877 −2.1848 −3.37217 0.026545 532 g27.t12329 g1583.t1 6.169854164 4.284198791 −2.89306 −2.18645 −3.371130.026568 1177 g10546.t1 3020 g6691.t1 K12196: VPS4 0 2.0553502662.102813 −2.18629 3.371236 0.026568 1178 g12603.t1 3021 g1139.t1 K13201:TIA1, 3.823455116 1.065757314 −2.74675 −2.18876 −3.3697 0.026622 TIAL11179 g2082.t1 3022 g2515.t1 4.08648863 0.419218481 −3.44889 −2.19514−3.36571 0.026769 1180 g4868.t1 3023 g4487.t1 K18106: GAAA 5.3413641481.56593075 −3.25482 −2.19916 −3.3632 0.026846 666 g9261.t1 2467g10439.t1 K01336: 4.328483282 2.215262412 −2.51243 −2.19953 −3.362970.026846 E3.4.21.48 1181 g4732.t1 3024 g2022.t1 3.266778123 7.9677845063.789697 −2.20442 3.359911 0.026965 1183 g8014.t1 3026 g3407.t1 K05994:5.396879706 0.439592246 −4.17848 −2.20633 −3.35872 0.026993 E3.4.11.101182 g2889.t1 3025 g10880.t1 5.096458376 2.729262266 −2.29259 −2.20614−3.35884 0.026993 1184 g6241.t1 3027 g7141.t1 2.980899445 5.573726682.99467 −2.20671 3.35848 0.026993 1185 g10185.t1 3028 g11141.t1 K12842:SR140 4.806643797 1.972250473 −3.66739 −2.20879 −3.35718 0.027029 1186g3181.t1 3029 g4963.t1 5.389590661 3.444021927 −2.6427 −2.20945 −3.356770.027036 1187 g1146.t1 3030 g259.t1 0 6.234452055 4.526416 −2.214413.353674 0.027156 1188 g3478.t1 3031 g4668.t1 K15118: 7.1881278070.666767656 −5.89063 −2.21606 −3.35264 0.027187 SLC25A38 1189 g10812.t13032 g11469.t1 4.970990313 1.431805036 −2.73708 −2.21814 −3.351350.027228 1190 g5729.t1 3033 g5268.t1 4.667119257 1.758398652 −2.50173−2.2199 −3.35025 0.027267 1191 g5773.t1 3034 g5183.t1 K18468: VPS352.974567603 0 −2.90432 −2.22779 −3.34532 0.027463 1192 g8342.t1 3035g5156.t1 7.147347587 4.289313069 −2.89998 −2.2316 −3.34294 0.027563 1193g2809.t1 3036 g9099.t1 8.970300194 3.622997906 −4.26489 −2.23498−3.34083 0.027638 1194 g3231.t1 3037 g6067.t1 5.450346027 0 −4.96789−2.23666 −3.33979 0.027676 1195 g15441.t1 3038 g27.t1 K02135: 04.22621488 3.724809 −2.238 3.338948 0.027703 ATPeF1E, ATP5E, ATP15 1196g4098.t1 3039 g3297.t1 6.95311286 0.150996268 −5.81014 −2.24117 −3.336970.027773 1197 g4149.t1 3040 g1830.t1 5.595722786 9.860906704 3.915612−2.24474 3.334743 0.027867 1198 g10768.t1 3041 g811.t1 K13281: uvsE,6.312249915 2.018280024 −3.29096 −2.24832 −3.33251 0.02795 UVE1 1199g6034.t1 3042 g11722.t1 3.569534287 0.521226153 −2.51415 −2.25484−3.32844 0.028085 1200 g7215.t1 3043 g5884.t1 K08141: MAL 4.1641690331.616753056 −2.47644 −2.26216 −3.32387 0.028255 1201 g8488.t1 3044g3354.t1 3.054782379 8.26554451 3.678738 −2.2697 3.319177 0.028434 1202g8852.t1 3045 g1260.t1 0.276187354 4.110227051 3.121435 −2.2707 3.3185490.028452 1203 g17481.t1 3046 g6577.t1 K03457: 4.118885089 0 −3.46084−2.27203 −3.31772 0.028471 TC.NCS1 1204 g6412.t1 3047 g5378.t1 06.454245699 4.80025 −2.27216 3.31764 0.028471 1205 g5249.t1 3048g2342.t1 4.593408785 2.333125085 −2.29042 −2.27289 −3.31719 0.0284811206 g4308.t1 3049 g1957.t1 K01934: E6.3.3.2 4.385816144 0.977864811−3.10874 −2.27469 −3.31607 0.028523 1207 g9497.t1 3050 g5756.t1 K12816:CDC40, 2.377976634 6.369846039 3.969675 −2.28074 3.312295 0.028645 PRP17480 g3149.t1 2377 g4998.t1 K01213: 0 4.972121854 5.052188 −2.290313.306327 0.028891 E.3.2.1.67 1208 g16357.t1 3051 g3292.t1 2.2746444496.642495757 3.654868 −2.29659 3.302412 0.029061 1209 g7653.t1 3052g7536.t1 K02218: CSNK1, 5.559496827 1.609655567 −3.10003 −2.29822−3.3014 0.029099 CK1 1210 g2461.t1 3053 g6733.t1 K17498: SPN1,4.599947501 0.537444052 −3.16588 −2.3086 −3.29493 0.0294 IWS1 1211g2212.t1 3054 g11601.t1 K15116: 4.637281551 2.751924072 −2.41127−2.31001 −3.29405 0.029419 SLC25A33_36, RIM2 1212 g10883.t1 3055 g172.t10 3.218252001 2.292182 −2.31043 3.293789 0.029419 1213 g7108.t1 3056g5573.t1 4.49020983 1.428868948 −5.17599 −2.31348 −3.29189 0.029502 1214g4692.t1 3057 g10596.t1 K00559: 5.217966775 0 −4.43958 −2.3144 −3.291320.029519 E2.1.1.41, SMT1, ERG6 1215 g7001.t1 3058 g6383.t1 0 3.2692779053.250609 −2.31504 3.29092 0.029526 1217 g11520.t1 3060 g4211.t1 K01273:5.534704503 1.679588747 −3.69176 −2.31962 −3.28807 0.029632 E3.4.13.19,DPEP1 1216 g470.t1 3059 g8009.t1 K03235: EF3, 2.63960049 0.413728279−3.66277 −2.31946 −3.28817 0.029632 TEF3 1218 g2297.t1 3061 g10716.t16.357052968 0.740815837 −4.61457 −2.32036 −3.2876 0.029643 1219 g7855.t13062 g10512.t1 5.263495212 2.246381404 −2.56985 −2.32321 −3.285830.029721 1221 g1216.t1 3064 g370.t1 7.767118225 5.274857999 −2.76524−2.326 −3.28409 0.029784 1220 g15283.t1 3063 g10473.t1 0.1481126383.597680572 3.864568 −2.32577 3.284235 0.029784 1222 g5238.t1 3065g2356.t1 8.469488529 1.842323775 −6.58325 −2.3311 −3.28092 0.029895 1223g16230.t1 3066 g10013.t1 6.19115729 1.549847227 −4.95006 −2.3385−3.27631 0.030121 1226 g14146.t1 3069 g3433.t1 5.134598916 0 −3.69373−2.33977 −3.27552 0.030123 1225 g882.t1 3068 g9407.t1 K12468: PAD15.834927879 7.524019066 3.111951 −2.33963 3.275605 0.030123 1224g10984.t1 3067 g5650.t1 0 3.058662563 3.407107 −2.33921 3.2758690.030123 1227 g6996.t1 3070 g6388.t1 K01104: 0 6.684739153 5.253925−2.34351 3.273191 0.030231 E3.1.3.48 1228 g4042.t1 3071 g3218.t1 K10426:DCTN4 3.476006591 0.824375553 −2.8745 −2.34446 −3.2726 0.030248 1229g10440.t1 3072 g8416.t1 4.661283453 2.396963708 −3.00648 −2.34837−3.27017 0.030363 1230 g3798.t1 3073 g9469.t1 6.108299926 1.801505479−3.74373 −2.35226 −3.26774 0.030434 1233 g5250.t1 3076 g2341.t14.192956387 2.110417944 −2.71795 −2.35314 −3.26719 0.030434 1231g17491.t1 3074 g10533.t1 2.340628751 5.104359936 3.343498 −2.352723.267457 0.030434 1232 g5149.t1 3075 g3828.t1 K11369: RTG2 2.7421677695.745670985 4.044872 −2.35272 3.267456 0.030434 1234 g10738.t1 3077g11985.t1 K10798: PARP 0 6.207294428 5.059725 −2.3571 3.264731 0.0304881235 g188.t1 3078 g5816.t1 K18342: OTUD6 4.706797138 1.42083914 −4.18554−2.35888 −3.26362 0.030533 678 g2539.t1 2558 g3572.t1 8.7651494356.260432332 −2.87811 −2.35928 −3.26338 0.030533 1236 g9576.t1 3079g6624.t1 K05355: hexPS, 0 2.554894937 3.221165 −2.36306 3.26102 0.030604COQ1 1237 g7963.t1 3080 g10258.t1 6.877809835 1.401061786 −5.00254−2.36399 −3.26044 0.030621 1238 g2081.t1 3081 g2516.t1 3.7483595970.609941541 −2.61083 −2.37166 −3.25567 0.030835 1239 g4635.t1 3082g2418.t1 4.337082348 1.030670213 −3.00281 −2.37336 −3.25461 0.0308781240 g1191.t1 3083 g351.t1 K14997: 0.860169772 4.900013294 2.978588−2.37713 3.252265 0.030977 SLC38A11 1241 g3500.t1 3084 g2191.t11.215931569 6.936301079 6.119258 −2.37828 3.251549 0.031002 1242g1860.t1 3085 g1884.t1 5.590523487 2.5557465 −2.92429 −2.37869 −3.251290.031002 1243 g7767.t1 3086 g891.t1 4.764291974 0.394275237 −5.55384−2.38214 −3.24915 0.031067 1244 g2268.t1 3087 g10684.t1 5.8637177730.278611595 −4.4083 −2.38343 −3.24835 0.03108 1245 g4613.t1 3088g7741.t1 K00463: INDO 1.444624706 3.80329617 2.176605 −2.38439 3.2477510.031098 683 g9852.t1 3089 g9791.t1 7.876191011 1.26909519 −2.81081−2.39122 −3.2135 0.031271 1246 g4349.t1 3090 g2121.t1 1.5322793587.011463446 4.872741 −2.39865 3.238883 0.03147 1247 g8581.t1 3091g6606.t1 K00558: 4.21948707 0.630336439 −5.33079 −2.40589 −3.234380.031676 DNMT1, dcm 1249 g9842.t1 3093 g9770.t1 K18576: XEG 6.1227957411.361365172 −6.17274 −2.40937 −3.23221 0.031754 1248 g2125.t1 3092g2952.t1 K01480: 4.351289056 1.416547398 −2.95902 −2.40906 −3.232410.031754 E3.5.3.11, speB 1250 g10362.t1 3094 g5453.t1 4.1536693971.595880592 −2.66682 −2.41506 −3.22868 0.031908 1257 g12070.t1 3101g7821.t1 K15356: VRG4, 4.864054909 0.460510026 −4.71756 −2.4197 −3.225790.031957 GONST1 1256 g4657.t1 3100 g2389.t1 5.666968159 0.321502083−4.36415 −2.41953 −3.2259 0.031957 1252 g6958.t1 3096 g6431.t1 K11968:ARIH1 3.357418226 0.095701333 −3.62143 −2.41882 −3.22634 0.031957 1253g19310.t1 3097 g9485.t1 5.087660505 2.997819493 −2.41441 −2.41917−3.22612 0.031957 1255 g10767.t1 3099 g12013.t1 K16833: PPP1R2.3.101333549 1.02165507 −2.06684 −2.41943 −3.22596 0.031957 IPP2 1251g11977.t1 3095 g12286.t1 5.145090044 8.173976979 2.420158 −2.418113.226784 0.031957 1254 g8978.t1 3098 g11390.t1 0 4.740307825 4.144828−2.41933 3.226023 0.031957 1258 g21710.t1 3102 g9500.t1 1.2389383873.734242323 3.209893 −2.42554 3.222163 0.032104 1259 g7491.t1 3103g10328.t1 3.324272702 0.292287423 −2.5088 −2.42722 −3.22112 0.0321491260 g7956.t1 3104 g10264.t1 6.737632146 0 −4.52249 −2.43476 −3.216430.032321 1261 g7964.t1 3105 g10257.t1 6.468663015 2.565678496 −3.82371−2.43516 −3.21619 0.032321 1262 g7455.t1 3106 g6879.t1 7.1336341762.350511691 −4.46812 −2.43579 −3.21579 0.032322 1264 g7919.t1 3108g8603.t1 7.707220525 5.344305103 −2.48556 −2.43812 −3.21434 0.0323621263 g6189.t1 3107 g9611.t1 3.290429112 6.571773343 2.859167 −2.437693.214609 0.032362 1265 g16176.t1 2509 g5232.t1 3.961883001 1.690859985−2.35469 −2.43856 −3.21407 0.032363 1266 g8674.t1 3109 g10950.t14.335667589 1.644834875 −2.29957 −2.43968 −3.21337 0.032377 1267g9656.t1 3110 g4870.t1 K12844: PRPF31 1.499922726 5.995240597 4.144522−2.44487 3.210148 0.032511 1268 g7488.t1 3111 g10325.t1 K11240: MSG54.501108392 0.613661381 −3.60908 −2.4515 −3.20603 0.032688 1269 g7672.t13112 g7571.t1 3.989155638 1.357471583 −3.34293 −2.45175 −3.205870.032688 1270 g55.t1 3113 g2746.t1 K14567: UTP14 5.127910319 6.9996463092.571354 −2.45654 3.2029 0.032843 1272 g9112.t1 3115 g3614.t17.062307238 0.410055385 −4.46156 −2.45932 −3.20117 0.0329 1271 g1753.t13114 g9720.t1 4.044374876 5.846317087 2.751402 −2.45908 3.201321 0.03291273 g10977.t1 3116 g5641.t1 K10735: GINS4, 4.051828119 8.6123931874.987555 −2.47134 3.193707 0.03327 SLD5 1274 g17737.t1 3117 g6552.t1K01893: NARS, 6.388427463 4.460451965 −2.16214 −2.47597 −3.190830.033354 asnS 1275 g10487.t1 3118 g1673.t1 K17774: MDM10 2.1647063824.843319565 3.625833 −2.47943 3.188681 0.033451 1276 g6558.t1 3119g10094.t1 K00643: 6.31176497 2.48933491 −3.18947 −2.48208 −3.187030.033532 E2.3.1.37, ALAS 1277 g2287.t1 3120 g9659.t1 4.385538556.941829687 3.216688 −2.4855 3.184907 0.033614 1278 g842.t1 3121g9463.t1 0 4.044547142 3.952811 −2.48774 3.18352 0.033652 1279 g2517.t13122 g3549.t1 5.937036867 2.027078484 −3.14005 −2.49094 −3.181530.033741 1280 g3451.t1 3123 g4694.t1 K18803: HPM1 7.6864389494.233781072 −2.70319 −2.49375 −3.17979 0.033786 1281 g6141.t1 3124g7301.t1 4.843357772 0.856838746 −3.43 −2.49677 −3.17791 0.033868 1282g12211.t1 3125 g8489.t1 4.086552127 0.933666875 −3.29049 −2.4978−3.17727 0.033888 1283 g9200.t1 3126 g6534.t1 6.260040742 2.764634545−2.90907 −2.50672 −3.17173 0.034162 1284 g5321.t1 3127 g2239.t17.891730863 3.602558714 −3.87368 −2.50755 −3.17122 0.034169 1285g3577.t1 3128 g3306.t1 7.444698622 1.243570464 −4.43732 −2.51028−3.16953 0.03425 1286 g16033.t1 3129 g8312.t1 K14961: RBBP5, 6.8143351390 −4.98563 −2.51933 −3.1639 0.034515 SWD1, CPS50 1287 g370.t1 3130g8886.t1 K05351: E1.1.1.9 2.495983173 0 −2.61273 −2.52005 −3.163460.034527 1288 g11747.t1 3131 g5055.t1 5.579800871 0 −5.65729 −2.52153−3.16254 0.034567 1289 g307.t1 3132 g9470.t1 K00450: 0 4.2969415093.379645 −2.52502 3.160374 0.034684 E1.13.11.4 1290 g4252.t1 3133g1730.t1 K14554: UTP21, 5.046177386 0 −4.35342 −2.52588 −3.159840.034692 WDR36 1291 g13249.t1 3134 g7068.t1 K00101: E1.1.2.3, 02.243022049 2.361545 −2.53745 3.152658 0.035035 lldD 1292 g97.t1 3135g2918.t1 K17550: PPP1R7, 6.872034629 1.343604487 −4.47691 −2.53859−3.15195 0.035064 SDS22 1293 g11152.t1 3136 g4836.t1 K01736: aroC4.537533205 12.27861396 6.435958 −2.54243 3.149569 0.035195 1294 g277.t13137 g11370.t1 0 3.079036559 2.875716 −2.54813 3.146033 0.035339 1296g1874.t1 3139 g4227.t1 3.147814191 5.126168567 2.979917 −2.555083.141723 0.035531 1295 g10285.t1 3138 g38.t1 0 3.651708721 6.254533−2.55454 3.142055 0.035531 1297 g7205.t1 3140 g5869.t1 K04712: DEGS3.678254356 0.752860849 −2.40347 −2.55623 −3.14101 0.035546 1298g3975.t1 3141 g7052.t1 K03127: TAF13 5.226674743 2.844506041 −3.29814−2.56215 −3.13733 0.035745 1299 g6129.t1 3142 g7317.t1 K18584: ACTR3,0.131743499 5.532439821 3.976918 −2.56833 3.133498 0.035969 ARP3 1300g1071.t1 3143 g8144.t1 K15163: SRB8, 9.338879184 2.598174135 −4.65483−2.57512 −3.12929 0.036158 MED12 1301 g9776.t1 3144 g933.t1 K18696: GDE14.318349985 2.568252231 −2.16956 −2.57518 −3.12925 0.036158 1302g9449.t1 3145 g10284.t1 K08286: 0.930122123 5.973997216 3.699965−2.57627 3.128576 0.036169 E2.7.11.- 1303 g8139.t1 3146 g11353.t15.695078874 3.389930558 −2.65431 −2.58118 −3.12553 0.036322 1304g3952.t1 3147 g3939.t1 3.467152816 8.346322304 4.395715 −2.582843.124498 0.036357 1306 g4583.t1 3149 g3309.t1 1.533947618 4.2929675222.896727 −2.58921 3.120549 0.036563 1305 g20261.t1 3148 g5213.t1 K15918:GLYK 0 1.938193397 3.648685 −2.58912 3.120602 0.036563 1307 g7529.t13150 g7276.t1 6.576826873 2.083647571 −4.58843 −2.5904 −3.11981 0.0365951308 g6754.t1 3151 g4367.t1 K02209: MCM5, 2.459200585 5.0551587242.751377 −2.5914 3.11919 0.036619 CDC46 1311 g491.t1 3154 g5498.t16.698116368 3.721035259 −3.28029 −2.59415 −3.11749 0.036659 1309g7837.t1 3152 g8557.t1 6.106640364 3.365204838 −2.32578 −2.59377−3.11772 0.036659 1310 g987.t1 3153 g8056.t1 0 3.027945316 3.671038−2.59389 3.117647 0.036659 1313 g17939.t1 3156 g10899.t1 6.8187079895.005569394 −2.67236 −2.60024 −3.11371 0.036861 1312 g2164.t1 3155g11903.t1 5.515137675 2.685444972 −2.26759 −2.5999 −3.11392 0.0368611314 g3906.t1 3157 g3985.t1 K03190: ureD, 2.671010414 5.335934882.738302 −2.60354 3.111663 0.036951 ureH 1315 g1097.t1 3158 g4041.t10.505695041 3.969049246 4.485033 −2.60467 3.110959 0.036981 1317g3623.t1 3160 g595.t1 K16466: CETN3 4.801115612 1.915084147 −3.20944−2.60598 −3.11015 0.036988 1316 g8411.t1 3159 g4430.t1 0 2.8105572222.579531 −2.60547 3.110465 0.036988 1318 g20530.t1 3161 g9496.t1 03.999056646 3.361046 −2.60652 3.109816 0.036994 1319 g1348.t1 3162g3450.t1 K10438: 3.588175282 1.235710845 −2.25653 −2.60816 −3.10880.037045 E1.14.13.63, phacB 1320 g3797.t1 3163 g2615.t1 6.0569869972.555508643 −2.7468 −2.61051 −3.10734 0.037124 1321 g7399.t1 3164g7182.t1 5.018202134 2.232656771 −2.93727 −2.61149 −3.10673 0.0371491322 g5488.t1 3165 g9822.t1 3.362985644 6.104316624 2.718614 −2.612093.106356 0.037158 1323 g9157.t1 3166 g6488.t1 K02324: POLE1 1.9737094274.469428234 3.333555 −2.61992 3.101503 0.037412 1324 g14847.t1 3167g1437.t1 K00641: metX 6.994074013 3.436994314 −2.90018 −2.63256 −3.093660.037835 1325 g6957.t1 3168 g6432.t1 K10746: EXO1 6.1311347010.388290481 −4.29624 −2.63704 −3.09089 0.037954 1326 g3447.t1 3169g4698.t1 4.987346272 1.724391306 −4.26254 −2.63726 −3.09075 0.0379541327 g9400.t1 3170 g3632.t1 4.819542549 7.125673734 3.137002 −2.637733.09046 0.037954 1328 g10198.t1 3171 g11163.t1 5.978274196 2.788975408−3.31916 −2.6404 −3.08881 0.038033 1331 g7497.t1 3174 g10332.t15.769438155 2.358653046 −3.94971 −2.64303 −3.08718 0.03808 1330 g7426.t13173 g7211.t1 K07151: STT3 6.089321429 2.57287541 −2.74784 −2.64279−3.08733 0.03808 1329 g8972.t1 3172 g11360.t1 K00949: thiN, 04.277976912 2.876826 −2.64269 3.087385 0.03808 TPK1, THI80 1332g11012.t1 3175 g5666.t1 0 5.38381861 3.856589 −2.6484 3.083847 0.0382551335 g2680.t1 3178 g4137.t1 K03305: TC.POT 4.251138075 0.905078368−3.52825 −2.65137 −3.08201 0.038301 1334 g12334.t1 3177 g7439.t14.832463772 1.425823624 −3.26532 −2.65114 −3.08215 0.038301 1333g4070.t1 3176 g3266.t1 K08502: VAM7 5.539846457 2.546984577 −2.7732−2.65099 −3.08224 0.038301 1336 g6026.t1 3179 g11719.t1 6.0958446520.68430684 −4.28462 −2.66367 −3.07438 0.038767 1337 g3846.t1 3180g3215.t1 5.151000423 1.006964699 −3.90954 −2.66555 −3.07322 0.03883 1338g5774.t1 3181 g5182.t1 4.645161281 0 −3.4513 −2.66704 −3.07229 0.0388771339 g3929.t1 3182 g3963.t1 K08866: TTK, 6.449588576 3.278968193−3.36947 −2.66843 −3.07143 0.03892 MPS1 1340 g2818.t1 3183 g9112.t15.23098229 2.042748595 −4.97039 −2.67161 −3.06946 0.038992 1341 g4639.t13184 g3141.t1 4.295463374 0 −3.88825 −2.67162 −3.06945 0.038992 1342g7766.t1 3185 g886.t1 1.950100615 −2.2513 −2.67226 −3.06906 0.039003K00276: AOC3, 3.696502907 AOC2, tynA 1343 g5178.t1 3186 g3785.t1 K10732:GINS1, 3.205102409 0.465489204 −2.9998 −2.67294 −3.06864 0.039016 PSF11344 g6934.t1 3187 g8796.t1 5.750734244 3.373972395 −2.72485 −2.67465−3.06758 0.039072 1345 g1969.t1 3188 g6228.t1 3.400168294 1.126194748−2.65712 −2.67603 −3.06672 0.039115 1346 g172.t1 3189 g12085.t1 K01531:E3.6.3.2, 6.497766777 1.752973654 −3.4052 −2.67672 −3.0663 0.039129mgtA, mgtB 1347 g11564.t1 3190 g4163.t1 K00274: MAO, 2.2005477245.983180821 3.284934 −2.67943 3.064613 0.039212 aofH 1348 g6920.t1 3191g6466.t1 K05607: AUH 3.935782227 1.559896558 −2.81933 −2.68386 −3.061870.039338 1349 g155.t1 3192 g5222.t1 K00129: E1.2.1.5 0 2.0386357342.662139 −2.68959 3.058314 0.039519 1351 g4054.t1 3194 g3233.t1 K00222:4.246709844 0.753125695 −3.82499 −2.6984 −3.05285 0.039787 TM7SF2, ERG241350 g259.t1 3193 g11071.t1 2.005826005 6.702898665 4.844188 −2.698073.053061 0.039787 1352 g2113.t1 3195 g6610.t1 5.320518398 1.691648425−3.58956 −2.70003 −3.05185 0.039841 1353 g18993.t1 3196 g1481.t16.460112374 2.188072612 −3.62105 −2.70385 −3.04948 0.039958 1354g9213.t1 3197 g9107.t1 K01535: E3.6.3.6 0.221964669 4.444533441 4.861882−2.70441 3.049135 0.039966 1355 g8608.t1 3198 g3036.t1 6.1711302112.686136331 −2.9841 −2.70848 −3.04661 0.040111 1359 g559.t1 3202g3897.t1 6.201870178 1.933937599 −3.99892 −2.71429 −3.04301 0.0402681357 g1111.t1 3200 g4058.t1 K17792: TIM54 5.442528526 1.477478055−3.04273 −2.71355 −3.04347 0.040268 1358 g2917.t1 3201 g5991.t15.742797006 3.575636867 −2.07424 −2.71393 −3.04323 0.040268 1356g13698.t1 3199 g7803.t1 K15015: 3.095824509 6.420340227 3.453954−2.71294 3.043849 0.040268 SLC32A, VGAT 1360 g3970.t1 3203 g9872.t1K14455: GOT2 6.495895484 1.144303422 −3.38447 −2.71544 −3.0423 0.0402871361 g6219.t1 3204 g7117.t1 K15030: EIF3M 9.064552828 7.245420142−3.3623 −2.71784 −3.04081 0.040375 1362 g9425.t1 3205 g10308.t1 K08850:AURKX 4.730673883 0.868742846 −4.27344 −2.72342 −3.03735 0.040551 1363g7501.t1 3206 g10336.t1 K18160: 5.345072335 0.733430789 −4.13019−2.72367 −3.03719 0.040551 NDUFAF2 1364 g859.t1 3207 g9445.t1 6.229640111.992693147 −3.27148 −2.72413 −3.03692 0.040555 1365 g1915.t1 3208g6151.t1 7.270928698 4.976410906 −2.43324 −2.73052 −3.03295 0.0407561366 g12217.t1 3209 g1989.t1 K00826: 3.918920739 1.387924318 −2.78762−2.73448 −3.0305 0.040915 E2.6.1.42. ilvE 1367 g4170.t1 3210 g1809.t10.622664993 6.671635624 3.839574 −2.74399 3.024609 0.041257 1368g9398.t1 2532 g3634.t1 4.794435739 1.682112273 −3.12889 −2.74644−3.02309 0.041334 1369 g11911.t1 3211 g11961.t1 4.426580032 0.838075179−3.7127 −2.75198 −3.01966 0.04155 1370 g1975.t1 3212 g6235.t1 K03676:grxC, 5.422460166 3.194829169 −2.95272 −2.75339 −3.01878 0.041581 GLRX,GLRX2 1371 g8163.t1 3213 g7963.t1 K16261: YAT 4.292364721 2.128178192−2.1584 −2.75419 −3.01829 0.041601 1372 g7701.t1 3214 g5632.t1 K16261:YAT 3.918348151 2.429142725 −2.02558 −2.76273 −3.013 0.041938 1373g9062.t1 3215 g8589.t1 0 4.231781639 4.010053 −2.76633 3.010768 0.0420681374 g21743.t1 3216 g11779.t1 K01969: 3.581364482 0.847557335 −4.15212−2.76857 −3.00938 0.042138 E6.4.1.4B 1375 g5576.t1 3217 g7494.t18.893181528 1.120853281 −5.86159 −2.77127 −3.00771 0.042212 1376g3089.t1 3218 g11792.t1 K00914: PIK3C3, 6.7596142 1.576374675 −4.25202−2.77342 −3.00637 0.042277 VPS34 1377 g5685.t1 3219 g1056.t1 K13524:ABAT 0 2.065375591 2.44012 −2.78145 3.001401 0.042547 1378 g4641.t1 3220g2414.t1 K03685: rnc, 0.412316469 4.991257678 3.332549 −2.78404 2.9997960.042649 DROSHA, RNT1 1379 g2363.t1 3221 g9258.t1 6.4866582481.454471294 −6.28212 −2.79029 −2.99592 0.042862 1380 g21382.t1 3222g5714.t1 K07734: paiB 6.462845057 2.264599961 −3.14521 −2.79042 −2.995840.042862 1381 g6400.t1 3223 g5394.t1 0 4.971894272 4.307014 −2.79322.994118 0.042975 1382 g10337.t1 3224 g56.t1 4.374119128 0.945262194−2.67548 −2.79768 −2.99134 0.043133 1383 g5528.t1 3225 g1657.t1 K02896:5.059362323 2.912712707 −2.81694 −2.80156 −2.98894 0.043281 RP-L24e,RPL24 1384 g11343.t1 3226 g11653.t1 K10981: POL4 6.259801244 1.648126626−4.35678 −2.80503 −2.98679 0.043411 1385 g5150.t1 3227 g3827.t12.931671142 5.392109666 3.102784 −2.81072 2.983263 0.043629 1386g6763.t1 3228 g4378.t1 K02321: POLA2 8.302494784 5.13409511 −2.44481−2.81189 −2.98254 0.043667 1387 g5671.t1 3229 g1071.t1 K11853: USP34 04.496504481 3.601192 −2.81539 2.98037 0.043799 1388 g11809.t1 3230g12052.t1 K11364: SGF29 3.463947854 6.116692885 2.833623 −2.816912.979429 0.043837 1389 g11797.t1 3231 g11951.t1 3.516751262 1.679255644−2.65677 −2.82277 −2.9758 0.044083 1390 g10681.t1 3232 g8527.t15.58963777 3.099515857 −2.57245 −2.82433 −2.97483 0.04413 1391 g4325.t13233 g11437.t1 13.11970013 2.933682888 −7.21408 −2.82725 −2.973020.044229 1392 g9381.t1 3234 g3653.t1 5.511774101 1.012685905 −3.81034−2.82909 −2.97188 0.044293 1393 g7852.t1 3235 g10509.t1 6.8827213165.021376437 −3.07319 −2.8293 −2.97175 0.044293 616 g5090.t1 2415g2954.t1 K08486: 0 3.867535804 3.836476 −2.8345 2.968529 0.044458STX1B_2_3 1394 g3829.t1 3236 g2598.t1 0.266144622 4.669261532 3.50036−2.8361 2.967538 0.044518 1395 g11535.t1 3237 g4192.t1 K17279:0.360331706 9.163288499 7.510402 −2.83657 2.967251 0.044524 REEP5_6 1396g6481.t1 3238 g5293.t1 K01886: QARS, 5.748896345 1.179880874 −5.49899−2.83881 −2.96586 0.044606 glnS 1397 g3005.t1 3239 g8297.t1 4.6601356750.923693205 −4.96111 −2.83903 −2.96573 0.044606 1398 g4078.t1 3240g3277.t1 3.936715366 2.213435275 −2.83788 −2.83933 −2.96554 0.0446061399 g2855.t1 3241 g9059.t1 K00627: DLAT, 5.436104451 0.350451845−3.90005 −2.84415 −2.96255 0.044805 accF, pdhC 1400 g3918.t1 3242g3974.t1 K00297: metF, 5.369411331 6.805636855 2.484666 −2.847832.960272 0.044957 MTHFR 1401 g7179.t1 3243 g566.t1 K09523: 0.6271781394.16165657 3.409315 −2.84799 2.960173 0.044957 DNAJC3 1402 g12408.t13244 g8249.t1 6.349198309 4.267606287 −4.36478 −2.85278 −2.9572 0.0451571403 g9652.t1 3245 g6915.t1 4.964995182 3.229940066 −3.59518 −2.85436−2.95623 0.045182 1404 g7523.t1 3246 g7288.t1 K13704: 1.2947555745.275553403 5.591409 −2.85471 2.95601 0.045182 ABHD12 1405 g14653.t13247 g2855.t1 5.738900905 1.835542251 −3.20682 −2.86057 −2.952380.045453 1406 g4096.t1 3248 g3295.t1 K17362: 4.848799761 1.091069648−3.86237 −2.86465 −2.94985 0.045602 ACOT13 1407 g18248.t1 3249 g2041.t14.35781588 7.901252086 3.784351 −2.86851 2.947457 0.045759 1408 g1237.t13250 g7426.t1 5.683015328 2.488598283 −2.99706 −2.87184 −2.945390.045853 1410 g3632.t1 3252 g608.t1 3.639980584 1.944176831 −2.64596−2.87251 −2.94498 0.045853 1409 g5562.t1 3251 g7477.t1 4.8103590529.131036427 4.168862 −2.87246 2.945014 0.045853 1411 g5477.t1 3253g8419.t1 K01876: DARS, 5.822436425 3.686550344 −3.1569 −2.87291 −2.944730.045855 aspS 1412 g9515.t1 3254 g6599.t1 K10729: SLD2 5.4704550542.40515865 −2.98726 −2.87443 −2.94379 0.045909 1413 g10318.t1 3255g72.t1 3.677226697 5.754668913 3.289688 −2.88275 2.938638 0.046244 1414g24.t1 3256 g12134.t1 2.224553826 7.898332502 4.242374 −2.8828 2.9386060.046244 1415 g8240.t1 3257 g10040.t1 K17784: 4.505441621 2.059214773−3.2426 −2.88456 −2.93751 0.046298 MINOS1, MOS1 1416 g7496.t1 3258g10330.t1 4.295198041 0.62681007 −4.62511 −2.88616 −2.93652 0.0463431418 g5019.t1 3260 g8992.t1 K00763: pncB, 5.789644312 0 −4.02631−2.88687 −2.93608 0.046344 NAPRT1 1417 g9422.t1 3259 g10311.t1 K17678:MRH4 4.99116655 2.76827123 −2.74095 −2.8868 −2.93613 0.046344 1419g6947.t1 3261 g6439.t1 4.318049534 0.859611004 −3.26378 −2.89495−2.93107 0.046698 1420 g1449.t1 3262 g6978.t1 7.510804913 5.552335444−3.23923 −2.89616 −2.93033 0.046742 1421 g11952.t1 3263 g5425.t1 K11886:ECM29 3.293996124 0.612527291 −2.70149 −2.90035 −2.92773 0.046902 1422g4463.t1 3264 g6821.t1 K03441: GLP-F 5.769121905 0.957880078 −3.49533−2.90325 −2.92593 0.047032 1423 g4565.t1 3265 g4096.t1 0.9190841125.08912066 3.486226 −2.90372 2.925643 0.047038 1424 g5152.t1 3266g3825.t1 3.965633731 9.790435178 4.134104 −2.9047 2.925032 0.047071 1425g5796.t1 3267 g4861.t1 4.412444745 6.978987815 2.714293 −2.9071 2.9235480.047159 1426 g2106.t1 3268 g2479.t1 K17877: NIT-6 4.4423820181.795290638 −2.90776 −2.90858 −2.92263 0.047216 1427 g2132.t1 3269g9887.t1 6.595948877 2.130028726 −3.56948 −2.91683 −2.91752 0.0475861428 g2743.t1 3270 g8874.t1 10.26584456 3.775688511 −5.63147 −2.91883−2.91628 0.047669 1429 g3255.t1 3271 g8226.t1 0 4.623799698 4.753278−2.91912 2.916098 0.047669 1430 g2515.t1 3272 g3546.t1 K03935:2.995934045 5.779005536 2.983913 −2.91952 2.915847 0.047672 NDUFS2 1431g11846.t1 3273 g8779.t1 5.108325438 0.456052036 −4.50763 −2.91997−2.91557 0.047677 1432 g4309.t1 3274 g1956.t1 K15436: TRPO3, 3.5127843840.746291622 −3.75578 −2.92157 −2.91458 0.047742 MTR10 1433 g342.t1 3275g8843.t1 K14617: 5.048487126 6.613903693 2.614424 −2.92704 2.911190.047918 LMBRD1 1434 g10330.t1 3276 g65.t1 K10592: 0 6.2175911334.494671 −2.92903 2.909954 0.048004 HUWE1, MULE, ARF-BP1 1435 g12736.t13277 g5713.t1 0 2.67764343 3.587796 −2.93123 2.908589 0.048101 1436g3120.t1 3278 g11825.t1 0 2.782475712 2.382813 −2.93213 2.9080340.048112 1437 g6122.t1 3279 g7325.t1 3.73309277 0 −3.82204 −2.93383−2.90698 0.048183 1438 g7506.t1 3280 g1313.t1 K02510: hpaI, 5.6813591132.954196465 −4.30541 −2.93555 −2.90591 0.048255 hpcH 1439 g4219.t1 3281g1764.t1 5.026702428 3.19824011 −2.28706 −2.93664 −2.90523 0.048294 1440g5995.t1 3282 g11694.t1 K08501: STX8 5.459232545 0.507403584 −3.61957−2.94175 −2.90207 0.048544 1441 g10838.t1 3283 g9836.t1 4.870398052.795973757 −2.14792 −2.94515 −2.89996 0.048705 626 g2308.t1 2425g10725.t1 5.237036425 3.494277968 −2.61152 −2.94809 −2.89814 0.0488251442 g6039.t1 3284 g11727.t1 K14809: DDX55, 5.042634955 2.144742508−3.54449 −2.95453 −2.89415 0.049112 SPB4 1443 g4021.t1 3285 g3194.t14.255555246 1.771901086 −3.07477 −2.95556 −2.89351 0.049148 1444g7825.t1 3286 g8668.t1 7.009481452 4.830504535 −2.37807 −2.95614−2.89315 0.049161 1445 g7886.t1 3287 g8663.t1 5.301291022 3.603605432−2.98612 −2.95905 −2.89135 0.049265 1446 g13691.t1 3288 g9725.t12.720405954 4.969707656 2.361023 −2.95911 2.891306 0.049265 1447g3039.t1 3289 g8267.t1 K14779: DDX52, 4.859751136 2.56647477 −2.80026−2.95956 −2.89103 0.049269 ROK1 1448 g5768.t1 3290 g5189.t1 K02948:RP-S11, 3.223518382 6.638489334 3.700189 −2.95986 2.890843 0.049269MRPS11, rpsK 1449 g8149.t1 3291 g7955.t1 7.075631425 1.400206991−4.60509 −2.96226 −2.88936 0.049369 1450 g13905.t1 3292 g4807.t15.937192138 4.105355745 −2.28795 −2.96241 −2.88926 0.049369 1451g9050.t1 3293 g5712.t1 0 1.428557276 2.850041 −2.96403 2.888256 0.0494371452 g11913.t1 3294 g658.t1 K14264: BNA3 3.176589195 0.818863118 −2.7115−2.96755 −2.88608 0.049608 1453 g11806.t1 3295 g12049.t1 K17260: ACTR2,3.412479141 8.573811497 4.004772 −2.96831 2.885605 0.049628 ARP2 “MedianExp. SYM00577” represents the median expression value in log2 tpm acrossbiological replicates of the beneficial Acremonium grown in mediainoculated with 50 mM PBS buffer. “Median Exp. SYM00300” represents themedian expression value in log2 tpm across biological replicates of theneutral Acremonium grown in media inoculated with 50 mM PBS buffer. “LogFC” represents the estimate of the log2-fold-change of the contrast.“B-statistic” represents the log-odds that the gene is differentiallyexpressed. “t-statistic” represents the moderated t-statistic. “Adj.p-value” represents the false discovery rate (Benjamini & Hochberg,1995) adjusted p-values.

TABLE 604 Median Exp. Median Exp. SEQ ID sym577 SEQ ID sym300 SYM00577SYM00577 SYM00577 gene SYM00300 gene Description Plant Mock 685 g6380.t12492 g764.t1 K05857: 3.20141475 5.073855922 PLCD 686 g857.t1 2491g9451.t1 K01950: 3.886920369 3.802514601 E6.3.5.1, NADSYN1, QNS1, nadE687 g13072.t1 2494 g9142.t1 0 0 675 g5348.t1 2554 g1.t1 5.703283097 0674 g5345.t1 2555 g9530.t1 K03510: 0 5.845894518 POLI 688 g68.t1 2495g909.t1 K00106: 6.788107371 7.003820996 XDH 689 g849.t1 2496 g9453.t1K06997: 2.698992601 3.120625144 K06997 690 g7926.t1 2497 g8597.t16.166677332 6.853860482 680 g1340.t1 2553 g523.t1 0 5.657989905 691g5563.t1 2493 g7478.t1 4.68326473 4.371792513 692 g5169.t1 2506 g3798.t14.28203011 4.865818268 677 g13489.t1 2556 g8733.t1 4.049293359 0 694g3058.t1 2499 g1604.t1 0 0 693 g2076.t1 2498 g2520.t1 3.9572315523.655783096 695 g3790.t1 2501 g2628.t1 K12486: 0 0 SMAP 676 g7741.t12557 g7091.t1 7.176505771 2.550284622 697 g852.t1 2502 g9454.t1 K11824:4.880882459 5.513795279 AP2A 696 g3920.t1 2508 g3972.t1 4.1277639965.062011561 678 g2539.t1 2558 g3572.t1 2.326788417 8.765149435 699g2257.t1 2504 g10668.t1 0 0 698 g657.t1 2503 g9863.t1 4.6882008624.4628192 Median Exp. Median Exp. SEQ ID SYM00300 SYM00300 Adj. SYM00577Plant Mock Log FC B-statistic t-statistic p-value 685 9.3593270160.295559632 10.14621 4.342538 10.54136 0.005738 686 0.5334500948.452816333 −8.12443 3.977388 −9.78835 0.005838 687 2.1374002528.254570732 −6.46147 3.201272 −8.45884 0.009315 675 4.0934457944.361478247 −5.78572 2.800585 −7.87932 0.009315 674 0.4721277470.825824927 5.241458 2.780518 7.851832 0.009315 688 7.7924333691.8413995 5.850131 2.994894 8.152802 0.009315 689 7.9632899780.692301308 7.186104 2.979489 8.13062 0.009315 690 8.6183396771.736488111 7.728272 2.846411 7.942614 0.009315 680 5.3081902842.558100341 8.898276 3.336937 8.669616 0.009315 691 9.926472681 08.941653 2.765035 7.830714 0.009315 692 6.198143572 0.928859379 6.2029922.4341 7.397597 0.014126 677 1.530959943 1.496465963 −3.96529 2.150927−7.05207 0.018531 694 5.62596164 1.924786245 3.932304 2.090546 6.9810830.018531 693 13.01166964 2.835668263 10.44786 2.127351 7.024242 0.018531695 6.121031288 1.019511648 5.080878 1.93808 6.80576 0.021595 6763.981693891 3.632045248 −4.74363 1.718895 −6.56295 0.02595 6977.286171288 2.276512626 5.32327 1.68203 6.523118 0.02595 696 6.3567887360.848055404 5.962067 1.696466 6.538681 0.02595 678 6.8735368496.260432332 7.696947 1.344744 6.171118 0.039348 699 3.91088716410.12999017 −6.28123 1.22348 −6.04968 0.042032 698 5.9255347061.558896118 4.563314 1.235076 6.061179 0.042032 This table describesorthologous genes of Acremonium zea sp. with beneficial and neutraleffects on soybean growth, these genes show significant genotypespecific changes in expression when grown in culture with and withoutplant homogenate. “Median Exp. SYM00577 Plant” represents the medianexpression value in log2 tpm across biological replicates of thebeneficial Acremonium grown in media inoculated with soybean seedlinghomogenate extracted with 50 mM PBS. “Median Exp. SYM00577 Mock”represents the median expression value in log2 tpm across biologicalreplicates of the beneficial Acremonium grown in media inoculated with50 mM PBS buffer. “Median Exp. SYM00300 Plant” seedling homogenateextracted with 50 mM PBS. “Median Exp. SYM00300” represents the medianexpression value in log2 tpm across biological replicates of the neutralAcremonium grown in media inoculated with soybean seedling homogenateextracted with 50 mM PBS. “Median Exp. SYM00300 Mock” represents themedian expression value in log2 tpm across biological replicates of theneutral Acremonium grown in media inoculated with 50 mM PBS buffer. “LogFC” represents the estimate of the log2-fold-change of the contrast.“B-statistic” represents the log-odds that the gene is differentiallyexpressed. “t-statistic” represents the moderated t-statistic. “Adj.p-value” represents the false discovery rate (Benjamini & Hochberg,1995) adjusted p-values.

TABLE 605 SEQ sym577 Median Exp. Median Exp. Adj. ID Description genePlant Mock Log FC B-statistic t-statistic p-value 674 K03510: g5345.t1 05.845894518 −5.48202 5.274576 −11.6138 0.002239 POLI 675 g5348.t15.703283097 0 5.589081 4.886533 10.76433 0.002344 677 g13489.t14.049293359 0 3.940048 4.438055 9.909633 0.002595 676 g7741.t17.176505771 2.550284622 5.088009 4.463602 9.955217 0.002595 678 g2539.t12.326788417 8.765149435 −7.03125 3.150667 −7.97247 0.014249 680 g1340.t10 5.657989905 −5.64042 2.991613 −7.77178 0.014249 679 K00275: g4287.t10.807562533 4.95193285 −4.19518 3.005051 −7.78848 0.014249 pdxH, PNPO681 K00574: g4581.t1 0.51190239 5.56764375 −4.84984 2.75309 −7.483060.017529 E2.1.1.79, cfa 682 K06874: g9772.t1 1.832873801 5.323512963−3.59486 2.657715 −7.37145 0.017819 K06874 683 g9852.t1 0.9399295417.876491011 −5.93834 2.189836 −6.85242 0.030523 684 g2536.t1 9.6718624212.653812149 6.993491 1.944631 6.59743 0.03853 This table describes genesof a Acremonium zea sp. with beneficial effects on soybean growth, thesegenes show significant changes in expression when grown in culture withand without plant homogenate. “Median Exp. Plant” represents the medianexpression value in log2 tpm across biological replicates grown in mediainoculated with soybean seedling homogenate extracted with 50 mM PBS.“Median Exp. Mock” represents the median expression value in log2_tpmacross biological replicates grown in media inoculated with 50 mM PBSbuffer. “Log FC” represents the estimate of the log2-fold-change of thecontrast. “B-statistic” represents the log-odds that the gene isdifferentially expressed. “t-statistic” represents the moderatedt-statistic. “Adj. p-value” represents the false discovery rate(Benjamini & Hochberg, 1995) adjusted p-values.

Example 7: Functional Characterization of Endophytes (SecretedProteomics Experiments)

This Example describes the ability of synthetic compositions comprisingplant seeds and a single endophyte strain or a plurality of endophytestrains described herein, to confer beneficial traits to a host plant.Among other things, this Example provides exemplary characterization ofmodulations in a beneficial endophyte's secretome, as compared to thesecretome of a neutral microbe of the same genus.

Mass spectrometry was used to explore differences in secreted proteinsbetween beneficial endophytes and neutral microbes. Four genera wereselected for the secreted proteomic analysis (two fungal and twobacterial): Acremonium, Phoma, Stenotrophomonas, and Agrobacterium. Foreach genus, a beneficial endophyte and neutral microbe were selected:SYM00577 (SEQ ID NO: 344) and SYM00300 (SEQ ID NO: 449); SYM15774 (SEQID NO: 447) and SYM01331 (SEQ ID NO: 450); SYM00906 (SEQ ID NO: 439) andSYM00865 (SEQ ID NO: 451); and SYM01004 (SEQ ID NO: 441) and SYM00091(SEQ ID NO: 427).

Microbes were cultivated in three biological replicates for each strain.Briefly, each bacterium was initially streaked on Reasoner's 2A (R2A)agar, distinct CFUs selected and cultured in 10 mL R2A broth for 4 days.Fungal strains were streaked on potato dextrose (PD) agar and individualplugs containing spores and mycelial tissues were used to initiategrowth in 10 mL PD broth for 6 days. All strains were grown withagitation at room temperature. Microbial culture filtrate was harvestedby centrifuging at 4500 RPM for 20 minutes in 15 mL Falcon tubes toallow culture separation and removal of the supernatant. Five mL ofculture supernatant were used for secreted proteomics analysis. Allsteps were performed in sterile conditions. Culture filtrates were keptin dry ice after harvest at all times to preserve protein stability.Media only samples consisting of PDB and R2A were tested independentlyto ensure the absence of intact proteins that could potentiallyinterfere with the secreted microbial peptides.

Prior to mass spectrometry, samples were concentrated on a Pall 3 kDMWCO MicroSep Spin Column (VWR Cat #89132-006) and quantified at 1:10dilution by Qubit fluorometry (Life Technologies). 12 μg of each samplewas separated ˜1.5 cm on a 10% Bis-Tris Novex mini-gel (Invitrogen)using the MES buffer system. The gel was stained with coomassie and eachlane was excised into ten equally sized segments.

Gel pieces were processed using a robot (ProGest, DigiLab) with thefollowing protocol:

Washed with 25 mM ammonium bicarbonate followed by acetonitrile.

Reduced with 10 mM dithiothreitol at 60° C. followed by alkylation with50 mM iodoacetamide at RT.

Digested with trypsin (Promega) at 37° C. for 4h.

Quenched with formic acid and the supernatant was analyzed directlywithout further processing.

Mass Spectrometry

The digests were analyzed by nano LC/MS/MS with a Waters NanoAcquityHPLC system interfaced to a ThermoFisher Q Exactive. Peptides wereloaded on a trapping column and eluted over a 75 μm analytical column at350 nL/min; both columns were packed with Proteo Jupiter resin(Phenomenex). A 30 min gradient was employed (5h total). The massspectrometer was operated in data-dependent mode, with MS and MS/MSperformed in the Orbitrap at 70,000 FWHM and 17,500 FWHM resolution,respectively. The fifteen most abundant ions were selected for MS/MS.

Data were searched using a local copy of Mascot with the followingparameters: Fixed modification: Carbamidomethyl (C); Variablemodifications: Oxidation (M), Acetyl (Protein N-term), Pyro-Glu (N-termQ), Deamidation (NQ); Mass values: Monoisotopic; Peptide Mass Tolerance:10 ppm; Fragment Mass Tolerance: 0.02 Da; Max Missed Cleavages: 2.

Mascot DAT files were parsed into the Scaffold software for validation,filtering and to create a non-redundant list per sample. Data werefiltered 1% protein and peptide level false discovery rate (FDR) andrequiring at least two unique peptides per protein.

Differential Secreted Protein Expression and Functional EnrichmentAnalysis

Data Acquisition and Processing

Protein sequence data, KEGG annotations and corresponding protein massspectrometry spectral count data were provided to a vendor. Data wereprovided for beneficial (A) and non-beneficial (B) species pairs fromtwo fungal and two bacterial genera. All data were converted into fileformats and a local database suitable for subsequent processing,analysis and parallelization.

Protein Ortholog Identification

Pairs/groups of orthologous proteins were identified using a modifiedversion of the OrthoMCL pipeline. Orthologs were identified asreciprocal best BLASTP hits, and then clusters of orthologous proteinswere defined using the modified OrthoMCL pipeline. This process was doneindependently for the within genera and the between genera analyses.BLASTP was run in parallel on the Georgia Tech PACE HPC environment.

Protein Functional Annotation

KEGG annotations for individual proteins were provided to the vendorbased on the whole genome sequence annotations. The program BLAST2GO wasused to annotate proteins with gene ontology (GO) terms based onsequence similarity to previously annotated proteins.

Protein Expression Quantification and Normalization

Individual protein expression levels were taken as the number ofobserved spectra (i.e. the spectra count) corresponding to each protein.Protein spectra counts were retrieved across three replicates for eachspecies. Missing counts for any given ortholog or replicate wereassigned values of 0. Individual protein expression levels (spectracounts) were then normalized by the total number of observed spectra foreach replicate. This process was done independently for the threereplicates corresponding to each member of the A-B pair of everyspecies. Fold-change (FC) values for orthologous pairs/groups werecomputed as log 2 A/B spectra counts for the purpose of functionalenrichment analysis

Protein Differential Expression Analysis

Differential protein expression analysis was done for a) pairs oforthologous proteins from the within genera analysis and b) groups oforthologous proteins from the between genera analysis. Differentialexpression was quantified by comparing the within group normalizedspectra count variation to the between group normalized spectra countvariation using the Students ttest. A Benjamini-Hochberg False DiscoverRate threshold of 0.2 was used to identify differentially abundantorthologous proteins.

Pathway and Functional Enrichment Analysis

Enrichment analysis was done in parallel using both KEGG and GOannotations with the hypergeometric test and via Gene Set EnrichmentAnalysis (GSEA). For the hypergeometric test, for any given functionalannotation category (i.e. KEGG pathway or GO term), the number ofproteins up-regulated in the beneficial member of the orthologous pair(species A) was compared to the total number of proteins up-regulated inthe complete set of orthologs. For GSEA analysis, orthologous proteinpairs/groups were ranked by FC values and the distribution of FC valueswas evaluated for a shift using the clusterprofiler R package.

SYM00577 Secreted Proteomic Analysis

TABLE 700 25 most abundant proteins secreted by SYM00577; “MedianAbundance” represents the median value across three biologicalreplicates in units of spectra per hundred spectra SEQ Median ID ProteinID Abundance GO Terms KEGG Terms 477 1AXg13463.t1 1.171575 GO:0008152:metabolic none process; GO:0016798: hydrolase activity, acting onglycosyl bonds 478 1AXg10805.t1 1.042072 GO:0004348: noneglucosylceramidase activity; GO:0005576: extracellular region;GO:0005975: carbohydrate metabolic process; GO:0006665: sphingolipidmetabolic process; GO:0030248: cellulose binding 479 1AXg10141.t10.63105 GO:0005975: carbohydrate none metabolic process; GO:0016787:hydrolase activity 480 1AXg3149.t1 0.581995 GO:0005975: carbohydrateKEGG Orthology: K01213: E3.2.1.67: galacturan metabolic process;1,4-alpha-galacturonidase [EC:3.2.1.67]; KEGG GO:0016798: hydrolasePATHWAY: ko00040: Pentose and glucuronate activity, acting on glycosylinterconversions:; KEGG PATHWAY: ko00500: bonds Starch and sucrosemetabolism: 481 1AXg5293.t1 0.516427 GO:0003723: RNA binding; KEGGOrthology: K01166: E3.1.27.1: ribonuclease GO:0033897: ribonuclease T2T2 [EC:3.1.27.1] activity; GO:0090502: RNA phosphodiester bondhydrolysis, endonucleolytic 482 1AXg10578.t1 0.498434 GO:0004190:aspartic-type none endopeptidase activity; GO:0006508: proteolysis 4831AXg10693.t1 0.404474 GO:0000328: fungal-type none vacuole lumen;GO:0016020: membrane; GO:0032366: intracellular sterol transport 4841AXg11973.t1 0.336207 GO:0005886: plasma none membrane; GO:0005975:carbohydrate metabolic process; GO:0016021: integral component ofmembrane; GO:0016740: transferase activity; GO:0016787: hydrolaseactivity; GO:0031225: anchored component of membrane 485 1AXg1240.t10.322054 GO:0003993: acid phosphatase KEGG Orthology: K01078: E3.1.3.2:acid activity; GO:0016311: phosphatase [EC:3.1.3.2]; KEGG PATHWAY:dephosphorylation; ko00627: Aminobenzoate degradation:; KEGG GO:0046872:metal ion binding PATHWAY: ko00740: Riboflavin metabolism:; KEGGPATHWAY: ko05152: Tuberculosis: Tuberculosis, or TB, is an infectiousdisease caused by Mycobacterium tuberculosis. One third of the world'spopulation is thought to be infected with TB. About 90% of thoseinfected result in latent infections, and about 10% of latent infectionsdevelop active diseases when their immune system is impaired due to theage, other diseases such as AIDS or exposure to immunosuppressive drugs.TB is transmitted through the air and primarily attacks the lungs, thenit can spread by the circulatory system to other parts of body. Once TBbacilli have entered the host by the respiratory route and infectedmacrophages in the lungs, they interfere with phagosomal maturation,antigen presentation, apoptosis and host immune system to establishpersistent or latent infection. 486 1AXg4516.t1 0.315618 GO:0005975:carbohydrate none metabolic process; GO:0016740: transferase activity;GO:0031224: intrinsic component of membrane 487 1AXg5358.t1 0.294999GO:0005976: polysaccharide KEGG Orthology: K01178: E3.2.1.3:glucoamylase metabolic process; [EC:3.2.1.3]; KEGG PATHWAY: ko00500:Starch GO:0016798: hydrolase and sucrose metabolism: activity, acting onglycosyl bonds; GO:0030246: carbohydrate binding 488 1AXg9478.t10.283328 GO:0044464: cell part none 489 1AXg3273.t1 0.275195 GO:0008233:peptidase activity KEGG Orthology: K01312: PRSS: trypsin [EC:3.4.21.4];KEGG PATHWAY: ko04080: Neuroactive ligand-receptor interaction:; KEGGPATHWAY: ko04972: Pancreatic secretion: The pancreas performs bothexocrine and endocrine functions. The exocrine pancreas consists of twoparts, the acinar and duct cells. The primary functions of pancreaticacinar cells are to synthesize and secrete digestive enzymes.Stimulation of the cell by secretagogues such as acetylcholine (ACh) andcholecystokinin (CCK) causes the generation of an intracellular Ca2+signal. This signal, in turn, triggers the fusion of the zymogengranules with the apical plasma membrane, leading to the polarisedsecretion of the enzymes. The major task of pancreatic duct cells is thesecretion of fluid and bicarbonate ions (HCO3-), which neutralize theacidity of gastric contents that enter the duodenum. An increase inintracellular cAMP by secretin is one of the major signals of pancreaticHCO3- secretion. Activation of the CFTR C1- channel and theCFTR-dependent C1-/ HCO3- exchange activities is responsible for cAMP-induced HCO3- secretion.; KEGG PATHWAY: ko04974: Protein digestion andabsorption: Protein is a dietary component essential for nutritionalhomeostasis in humans. Normally, ingested protein undergoes a complexseries of degradative processes following the action of gastric,pancreatic and small intestinal enzymes. The result of this proteolyticactivity is a mixture of amino acids and small peptides. Amino acids(AAs) are transported into the enterocyte (intestinal epithelial cell)by a variety of AA transporters that are specific for cationic (basic)AA, neutral AA, and anionic (acidic) AA. Small peptides are absorbedinto enterocytes by the PEPT1 transporter. Inside enterocytes peptidesare hydrolyzed, and the resulting amino acids are released together withthose absorbed by AA transporters into blood via multiple, basolateral,AA transporters. Hydrolysis-resistant peptides, however, are transportedout of the cells by a basolateral peptide transporter that has not beenidentified molecularly.; KEGG PATHWAY: ko05164: Influenza A: Influenzais a contagious respiratory disease caused by influenza virus infection.Influenza A virus is responsible for both annual seasonal epidemics andperiodic worldwide pandemics. Novel strains that cause pandemics arisefrom avian influenza virus by genetic reassortment among influenzaviruses and two surface glycoproteins HA and NA form the basis ofserologically distinct virus types. The innate immune system recognizesinvaded virus through multiple mechanisms. Viral non-structural NS1protein is a multifunctional virulence factor that interfere IFN-mediated antiviral response. It inhibits IFN production by blockingactivation of transcription factors such as NF-kappa B, IRF3 and AP1.NS1 further inhibits the activation of IFN-induced antiviral genes.PB1-F2 protein is another virulence factor that induce apoptosis ofinfected cells, which results in life-threatening bronchiolitis. 4901AXg8115.t1 0.234864 GO:0008152: metabolic process; none GO:0016787:hydrolase activity 491 1AXg12530.t1 0.232187 GO:0000103: sulfate KEGGOrthology: K03671: trxA: thioredoxin 1 assimilation; GO:0005634:nucleus; GO:0005829: cytosol; GO:0006457: protein folding; GO:0015035:protein disulfide oxidoreductase activity; GO:0016671: oxidoreductaseactivity, acting on a sulfur group of donors, disulfide as acceptor;GO:0034599: cellular response to oxidative stress; GO:0044281: smallmolecule metabolic process; GO:0045454: cell redox homeostasis;GO:0055114: oxidation-reduction process; GO:0071704: organic substancemetabolic process; GO:1900429: negative regulation of filamentous growthof a population of unicellular organisms 492 1AXg9266.t1 0.218366GO:0016491: oxidoreductase none activity 493 1AXg12742.t1 0.214329GO:0004553: hydrolase none activity, hydrolyzing O- glycosyl compounds;GO:0071704: organic substance metabolic process 494 1AXg6959.t1 0.213513GO:0004190: aspartic-type none endopeptidase activity; GO:0006508:proteolysis 495 1AXg936.t1 0.208768 GO:0008152: metabolic none process;GO:0019239: deaminase activity 496 1AXg13882.t1 0.208427 GO:0008152:metabolic KEGG Orthology: K01078: E3.1.3.2: acid process; GO:0016788:phosphatase [EC:3.1.3.2]; KEGG PATHWAY: hydrolase activity, acting onko00627: Aminobenzoate degradation:; KEGG ester bonds PATHWAY: ko00740:Riboflavin metabolism:; KEGG PATHWAY: ko05152: Tuberculosis:Tuberculosis, or TB, is an infectious disease caused by Mycobacteriumtuberculosis. One third of the world's population is thought to beinfected with TB. About 90% of those infected result in latentinfections, and about 10% of latent infections develop active diseaseswhen their immune system is impaired due to the age, other diseases suchas AIDS or exposure to immunosuppressive drugs. TB is transmittedthrough the air and primarily attacks the lungs, then it can spread bythe circulatory system to other parts of body. Once TB bacilli haveentered the host by the respiratory route and infected macrophages inthe lungs, they interfere with phagosomal maturation, antigenpresentation, apoptosis and host immune system to establish persistentor latent infection. 497 1AXg9750.t1 0.191554 GO:0005576: extracellularnone region; GO:0030248: cellulose binding; GO:0045493: xylan catabolicprocess; GO:0046373: L-arabinose metabolic process; GO:0046556: alpha-L-arabinofuranosidase activity 498 1AXg6573.t1 0.188047 GO:0004568:chitinase activity; none GO:0005975: carbohydrate metabolic process;GO:0006032: chitin catabolic process 499 1AXg92.t1 0.186476 GO:0016998:cell wall none macromolecule catabolic process; GO:0052861: glucanendo-1,3-beta-elucanase activity, C-3 substituted reducing group;GO:0052862: glucan endo-1,4-beta- glucanase activity, C-3 substitutedreducing group 500 1AXg9192.t1 0.167015 GO:0005975: carbohydrate nonemetabolic process 501 1AXg11043.t1 0.1663 GO:0003824: catalyticactivity; none GO:0044238: primary metabolic process; GO:0071704:organic substance metabolic process

SYM00577 Versus SYM00300

TABLE 701 Differential secreted protein abundance between SYM00577 andSYM00300. SEQ ID SEQ FDR Ben- ID q- efi- Neu- A. B. Fold- val- cialA.protein tral B.protein KEGG GO mean mean change absFC ue 5021AXg1022.t1 2297 1BXg8091.t1 Biosynthesis of amino acids, carbohydratemetabolic process, 0 0.37 −8.5 8.5 0.03 Carbon metabolism, cytosol,nucleus, pentose- E2.2.1.2. talA, talB phosphate shunt, non-oxidativePentose phosphate pathway branch, sedoheptulose-7- phosphate:D-glyceraldehyde-3- phosphate glyceronetransferase activity 4871AXg5358.t1 2298 1BXg9546.t1 E3.2.1.3, Starch and sucrose carbohydratebinding, hydrolase 0.3 0 8.2 8.2 0.02 metabolism activity, acting onglycosyl bonds, polysaccharide metabolic process 503 1AXg8841.t1 22991BXg1271.t1 Cysteine and methionine adenosylhomocysteinase 0 0.24 −7.97.9 0.01 metabolism, E3.3.1.1, ahcY activity cytosol, one-carbonmetabolic process, phosphatidylcholine biosynthetic process,S-adenosylhomocysteine catabolic process, triglyceride metabolic process504 1AXg20808.t1 2300 1BXg8757.t1 None carbohydrate metabolic 0 0.24−7.9 7.9 0.02 process, hydrolase activity, acting on glycosyl bonds,hydrolase activity, hydrolyzing O-glycosyl compounds, metabolic process505 1AXg10583.t1 2301 1BXg10631.t1 None cell wall macromolecule 0.16 07.4 7.4 0.05 catabolic process, lysozyme activity, peptidoglycancatabolic process 506 1AXg8644.t1 2302 1BXg2276.t1 E3.1.27.1 cytoplasmicpart, ribonuclease 0 0.13 −7.1 7.1 0.02 T2 activity, RNA binding, RNAphosphodiester bond hydrolysis, endonucleolytic, single- organismcellular process 507 1AXg360.t1 2303 1BXg8875.t1 None None 0 0.12 −6.96.9 0.01 508 1AXg9960.t1 2304 1BXg11250.t1 Purine metabolism, ylbA, None0 0.12 −6.9 6.9 0.02 UGHY 509 1AXg10066.t1 2305 1BXg2721.t1 Nonenuclease activity 0 0.12 −6.9 6.9 0.03 510 1AXg9954.t1 2306 1BXg11402.t1None hydrolase activity, metabolic 0 0.12 −6.9 6.9 0.04 process 5111AXg11078.t1 2307 1BXg1562.t1 None None 0 0.1 −6.7 6.7 0.02 5121AXg7161.t1 2308 1BXg550.t1 Aminobenzoate degradation, None 0 0.1 −6.76.7 0.02 Folate biosynthesis, phoD, Two-component system 513 1AXg7978.t12309 1BXg10240.t1 None hydrolase activity 0 0.09 −6.6 6.6 0.02 5141AXg8599.t1 2310 1BXg3056.t1 None None 0.1 0 6.6 6.6 0.02 5151AXg11864.t1 2311 1BXg8819.t1 None glucose metabolic process, L- 0 0.1−6.6 6.6 0.02 xylulose reductase (NADP+) activity, mannitol 2-dehydrogenase (NADP+) activity, mitochondrion, oxidation-reductionprocess, protein homotetramerization, xylulose metabolic process 5161AXg13464.t1 2312 1BXg8758.t1 None hydrolase activity, metabolic 0 0.09−6.6 6.6 0.02 process 517 1AXg13099.t1 2313 1BXg8761.t1 Nonecarbohydrate metabolic process, 0 0.09 −6.5 6.5 0.02 hydrolase activity,hydrolyzing O-glycosyl compounds, intracellular part 518 1AXg10728.t12314 1BXg4259.t1 None hydrolase activity, metabolic 0.09 0 6.5 6.5 0.05process 519 1AXg31.t1 2315 1BXg2840.t1 gcvH, GCSH, Glycine, glycinecleavage complex, 0 0.08 −6.4 6.4 0.02 serine and threonine glycinedecarboxylation via metabolism, Glyoxylate and glycine cleavage system,dicarboxylate metabolism mitochondrion, one-carbon metabolic process,oxidation- reduction process, protein lipoylation 520 1AXg4476.t1 23161BXg5721.t1 None endonuclease activity, 0 0.09 −6.4 6.4 0.02 exonucleaseactivity, nuclease activity, nucleic acid phosphodiester bond hydrolysis521 1AXg11059.t1 2317 1BXg2900.t1 Fatty acid elongation, endoplasmicreticulum, 0.08 0 6.3 6.3 0.02 Fatty acid metabolism,palmitoyl-(protein) hydrolase Lysosome, PPT activity, proteindepalmitoylation, vacuolar acidification, vacuole 522 1AXg10328.t1 23181BXg8689.t1 None None 0 0.06 −6 6 0.01 523 1AXg10740.t1 23191BXg11987.t1 None cell part 0 0.24 −6 6 0.02 524 1AXg18392.t1 23201BXg11664.t1 Adrenergic signaling in ascospore-type prospore- 0 0.06 −66 0.03 cardiomyocytes, Alcoholism, specific spindle pole bodyAlzheimer′s disease, remodeling, ATP hydrolysis Amphetamine addictioncoupled proton transport, Calcium signaling pathway, barrier septum,calcium ion CALM, cAMP signaling binding, calcium-dependent pathway,cGMP-PKG protein binding, cell budding, signaling pathway, Circadiancell division site, cellular bud entrainment, Dopaminergic neck,cellular bud tip, central synapse, Estrogen signaling plaque of spindlepole body, pathway, Gastric acid cytosol, hydrogen ion secretion,Glioma, GnRH transmembrane transporter signaling pathway, activity,incipient cellular bud Inflammatory mediator site, integral component ofregulation of TRP channels, membrane, karyogamy involved Insulinsignaling pathway, in conjugation with cellular Long-term potentiation,fusion, lysosomal Metanogenesis, microautophagy, maintenanceNeurotrophin signaling of protein location in spindle pathway, Olfactorypole body, mating projection transduction, Oocyte tip, mitotic spindleassembly, meiosis, Oxytocin signaling mitotic spindle pole body,pathway, Pertussis, mycelium development, new Phosphatidylinositolgrowing cell tip, NLS-bearing signaling system, protein import intonucleus, Phototransduction, nucleus, old growing cell tip,Phototransduction - fly, phosphatidylinositol Plant-pathogeninteraction, biosynthetic process, proton- Rap1 signaling pathway, Rastransporting V-type ATPase, signaling pathway, Salivary V0 domain,receptor-mediated secretion, Tuberculosis, endocytosis, regulation ofcell Vascular smooth muscle cycle, spitzenkorper, spore contractiongermination, transcription factor import into nucleus, vacuole fusion,non-autophagic 525 1AXg3446.t1 2321 1BXg4699.t1 None None 0 0.06 −6 60.03 526 1AXg3959.t1 2322 1BXg3931.t1 Amino sugar and nucleotidehydrolase activity, hydrolyzing 0 0.06 −6 6 0.04 sugar metabolism,E3.2.1.14 O-glycosyl compounds, organic substance metabolic process 4941AXg6959.t1 2323 1BXg7026.t1 None aspartic-type endopeptidase 0.23 0 5.95.9 0.02 activity, proteolysis 527 1AXg4985.t1 2324 1BXg8953.t1 None FMNbinding, oxidation- 0 0.06 −5.9 5.9 0.04 reduction process,oxidoreductase activity 528 1AXg4291.t1 2325 1BXg1944.t1 E3.2.1.101hydrolase activity 0.05 0 5.8 5.8 0.02 529 1AXg6728.t1 2326 1BXg4339.t1ndk, NME, Purine ATP binding, CDP 0 0.06 −5.8 5.8 0.02 metabolism,Pyrimidine phosphorylation, cellular metabolism response to DNA damagestimulus, CTP biosynthetic process, cytosol, GTP biosynthetic process,identical protein binding, integral component of membrane, mitochondrialintermembrane space, nucleoside diphosphate kinase activity, nucleus,UTP biosynthetic process 530 1AXg10268.t1 2327 1BXg2378.t1 Nonehydrolase activity, acting on 0.05 0 5.8 5.8 0.02 glycosyl bonds,metabolic process 531 1AXg3277.t1 2328 1BXg3155.t1 None hydrolaseactivity, membrane 0.06 0 5.8 5.8 0.03 532 1AXg27.t1 2329 1BXg1583.t1None acid phosphatase activity, 0 0.05 −5.8 5.8 0.04 dephosphorylation533 1AXg1627.t1 2330 1BXg7861.t1 None cell redox homeostasis, Golgi 00.05 −5.7 5.7 0.02 trans cisterna, integral component of plasmamembrane, oligopeptide transport, oligopeptide transporter activity,peroxisome, positive regulation of monopolar cell growth, regulation ofphosphoslipid translocation, regulation of vacuole organization,transmembrane transport, vacuole fusion, non-autophagic 534 1AXg5235.t12331 1BXg2358.t1 Antigen processing and ATP binding, integral 0 0.05−5.7 5.7 0.02 presentation, Endocytosis, component of membraneEpstein-Barr virus infection, Estrogen signaling pathway, HSPA1_8,Influenza A, Legionellosis, MAPK signaling pathway, Measles, Proteinprocessing in endoplasmic reticulum, Spliceosome, Toxoplasmosis 5351AXg7693.t1 2332 1BXg9970.t1 None carbohydrate binding, 0 0.05 −5.7 5.70.03 carbohydrate catabolic process, hydrolase activity, hydrolyzingO-glycosyl compounds 536 1AXg7827.t1 2333 1BXg8670.t1 Ribosome, RP-S16e,RPS16 ribosome, structural constituent 0 0.05 −5.6 5.6 0.02 of ribosome,translation 537 1AXg9662.t1 2334 1BXg4876.t1 None integral component of0 0.05 −5.6 5.6 0.02 membrane, transmembrane transport, transmembranetransporter activity 538 1AXg5289.t1 2335 1BXg2280.t1 Alanine, aspartateand calmodulin binding, cellular 0 0.05 −5.6 5.6 0.02 glutamatemetabolism, beta- response to oxidative stress, Alanine metabolism,cytoplasm, glutamate catabolic Butanoate metabolism, process, glutamateE4.1.1.15, gadB, gadA, decarboxylase activity, GAD, GABAergic synapse,pyridoxal phosphate binding Taurine and hypotaurine metabolism, Type Idiabetes mellitus 539 1AXg10486.t1 2336 1BXg1674.t1 SLC39A1_2_3,ZIP1_2_3 integral component of 0 0.05 −5.6 5.6 0.03 membrane,low-affinity zinc II ion transport, low-affinity zinc ion transmembranetransporter activity, plasma membrane, zinc II ion transmembranetransport, zinc ion transmembrane transporter activity 540 1AXg12100.t12337 1BXg7176.t1 Cell cycle, Epstein-Barr monooxygenase activity, 0 0.05−5.6 5.6 0.03 virus infection, Hippo oxidation-reduction process,signaling pathway, Hippo protein domain specific binding signalingpathway - fly, Neurotrophin signaling pathway, Oocyte meiosis, PI3K-Aktsignaling pathway, Viral carcinogenesis, YWHAE 541 1AXg5383.t1 23381BXg9570.t1 Alzheimer′s disease, glucose metabolic process, 0 0.05 −5.55.5 0.02 Biosynthesis of amino acids, glyceraldehyde-3-phosphate Carbonfixation in dehydrogenase (NAD+) photosynthetic organisms,(phosphorylating) activity, Carbon metabolism, glycolytic process, NADGAPDH, gapA, binding, NADP binding, Glycolysis/Gluconeogenesis,oxidation-reduction process HIF-1 signaling pathway 542 1AXg10197.t12339 1BXg11161.t1 E3.1.4.46, glpQ, ugpQ, glycerophosphodiester 0 0.04−5.4 5.4 0.01 Glycerophospholipid phosphodiesterase activity, metabolismlipid metabolic process 543 1AXg4433.t1 2340 1BXg6768.t1 E3.2.1.6hydrolase activity, hydrolyzing 0 0.04 −5.4 5.4 0.04 O-glycosylcompounds, metabolic process 544 1AXg3932.t1 2341 1BXg3960.t1 FoxOsignaling pathway, cytosol, identical protein 0 0.04 −5.4 5.4 0.04 PRMT1binding, mRNA export from nucleus, negative regulation of DNA-templatedtranscription, termination, nucleus, peptidyl- arginine methylation, toasymmetrical-dimethyl arginine, positive regulation of transcriptionelongation from RNA polymerase II promoter, protein-arginine omega-Nasymmetric methyltransferase activity, protein-arginine omega-Nmonomethyltransferase activity 545 1AXg10561.t1 2342 1BXg1546.t1 Noneoxidoreductase activity 0 0.04 −5.3 5.3 0.02 546 1AXg3216.t1 23431BXg6110.t1 None lipid metabolic process, organic 0 0.04 −5.3 5.3 0.05substance metabolic process, phosphoric diester hydrolase activity,primary metabolic process 547 1AXg7277.t1 2344 1BXg11845.t1 EEF1A,Legionellosis, cytoplasm, GTP binding, 0 0.04 −5.2 5.2 0.02 RNAtransport GTPase activity, translation elongation factor activity,translational elongation 548 1AXg10803.t1 2345 1BXg2053.t1 Nonecarbohydrate metabolic process, 0 0.04 −5.2 5.2 0.02 cellulose binding,extracellular region, hydrolase activity, hydrolyzing O-glycosylcompounds 549 1AXg6123.t1 2346 1BXg7324.t1 None None 0 0.04 −5.2 5.20.02 550 1AXg4834.t1 2347 1BXg4445.t1 None carbohydrate metabolicprocess, 0.03 0 5.1 5.1 0.02 hydrolase activity, hydrolyzing O-glycosylcompounds, integral component of membrane 551 1AXg13304.t1 23481BXg9661.t1 None carbohydrate metabolic process, 0.01 0.19 −5 5 0.01hydrolase activity, hydrolyzing O-glycosyl compounds 552 1AXg3171.t12349 1BXg2692.t1 E3.2.1.4, Starch and sucrose hydrolase activity,hydrolyzing 0 0.03 −5 5 0.02 metabolism O-glycosyl compounds,polysaccharide catabolic process 553 1AXg7126.t1 2350 1BXg5592.t1 Aminosugar and nucleotide ATP binding, canonical 0 0.03 −5 5 0.04 sugarmetabolism, Butirosin glycolysis, carbohydrate and neomycinbiosynthesis, phosphorylation, cellular Carbohydrate digestion andglucose homeostasis, cytosol, absorption, Carbon fructokinase activity,fructose metabolism, Central carbon 6-phosphate metabolic process,metabolism in cancer, fructose import, fructose Fructose and mannosemetabolic process, glucokinase metabolism, Galactose activity, glucose6-phosphate metabolism, Glycolysis/ metabolic process, glucoseGluconeogenesis, HIF-1 binding, glucose import, signaling pathway, HK,mannokinase activity, mannose Insulin signaling pathway, metabolicprocess, Starch and sucrose mitochondrion, nucleus, metabolism,Streptomycin regulation of transcription by biosynthesis, Type IIglucose, replicative cell aging diabetes mellitus 554 1AXg1749.t1 23511BXg9726.t1 None None 0 0.03 −4.9 4.9 0.02 555 1AXg10973.t1 23521BXg5639.t1 K16330, Pyrimidine cytoplasm, endonucleolytic 0 0.03 −4.94.9 0.02 metabolism cleavage in 5′-ETS of tricistronic rRNA transcript(SSU-rRNA, 5.8S rRNA, LSU-rRNA), endonucleolytic cleavage in ITS1 toseparate SSU-rRNA from 5.8S rRNA and LSU-rRNA from tricistronic rRNAtranscript (SSU-rRNA, 5.8S rRNA, LSU-rRNA), endonucleolytic cleavage togenerate mature 5′-end of SSU-rRNA from (SSU-rRNA, 5.8S rRNA, LSU-rRNA),hydrolase activity, acting on glycosyl bonds, kinase activity,phosphorylation, pseudouridine synthesis, Pwp2p-containing subcomplex of90S peribosome, small-subunit processome 556 1AXg2695.t1 23531BXg6589.t1 None None 0 0.03 −4.9 4.9 0.03 557 1AXg5845.t1 23541BXg1158.t1 Ribosome, RP-S3e, RPS3 cytoplasmic translation, 0 0.03 −4.94.9 0.04 cytosolic small ribosomal subunit, DNA catabolic process,endonucleolytic, DNA- (apurinic or apyrimidinic site) lyase activity,preribosome, small subunit precursor, ribosomal small subunit exportfrom nucleus, RNA binding, rRNA export from nucleus, structuralconstituent of ribosome 558 1AXg9065.t1 2355 1BXg8585.t1 AMPK signalingpathway, GTP binding, GTPase activity, 0 0.03 −4.9 4.9 0.04 EEF2,Oxytocin signaling integral component of pathway membrane, translationelongation factor activity, translational elongation 559 1AXg10539.t12356 1BXg6684.t1 None None 0 0.03 −4.8 4.8 0.02 560 1AXg4683.t1 23571BXg10580.t1 E3.2.1.8, xynA D-xylose metabolic process, 0 0.03 −4.8 4.80.02 endo-1,4-beta-xylanase activity, xylan catabolic process 5611AXg1198.t1 2358 1BXg352.t1 Adherens junction, Axon 1,3-beta-D-glucansynthase 0 0.03 −4.8 4.8 0.04 guidance, Bacterial invasion complex,actin cytoskeleton of epithelial cells, cAMP reorganization, buddingcell signaling pathway, cGMP- bud growth, cellular bud neck, PKGsignaling pathway, cellular bud tip, Golgi Chemokine signalingapparatus, GTP binding, pathway, Colorectal cancer, GTPase activity,incipient Endocytosis, Focal adhesion, cellular bud site, matingLeukocyte transendothelial projection tip, peroxisome, migration, MAPKsignaling positive regulation of pathway - yeast, MicroRNAs endocytosis,positive regulation in cancer, Neurotrophin of protein kinase Csignaling, signaling pathway, Oxytocin protein transport, regulation ofsignaling pathway, cell size, regulation of cell wall Pancreaticsecretion, (1 -> 3)-beta-D-glucan Pathogenic Escherichia colibiosynthetic process, regulation infection, Pathways in of exocystlocalization, cancer, Pertussis, Platelet regulation of fungal-type cellactivation, Proteoglycans in wall organization, regulation of cancer,Rap1 signaling vacuole fusion, non-autophagic, pathway, Ras signalingsmall GTPase mediated signal pathway, Regulation of actin transductioncytoskeleton, RHOA, Sphingolipid signaling pathway, T cell receptorsignaling pathway, TGF-beta signaling pathway, Tight junction,Tuberculosis, Vascular smooth muscle contraction, Viral carcinogenesis,Wnt signaling pathway 562 1AXg1904.t1 2359 1BXg5010.t1 YAT amino acidtransmembrane 0 0.03 −4.7 4.7 0.02 transport, amino acid transmembranetransporter activity, integral component of membrane 563 1AXg3176.t12360 1BXg4958.t1 HXT, Meiosis - yeast integral component of membrane, 00.02 −4.6 4.6 0.02 substrate-specific transmembrane transporteractivity, transmembrane transport 564 1AXg10060.t1 2361 1BXg2791.t1E3.2.1.8, xynA endo-1,4-beta-xylanase activity, 0 0.02 −4.5 4.5 0.02xylan catabolic process 565 1AXg5709.t1 2362 1BXg9980.t1 2-Oxocarboxylicacid 3-isopropylmalate 0 0.02 −4.5 4.5 0.02 metabolism, Biosynthesis ofdehydrogenase activity, ATP amino acids, C5-Branched binding, ATPhydrolysis dibasic acid metabolism, coupled proton transport, ATP leuB,Valine, leucine and metabolic process, cytosol, isoleucine biosynthesisglyoxylate cycle, leucine biosynthetic process, magnesium ion binding,NAD binding, oxidation-reduction process, proton-transporting in ATPaseactivity, rotational mechanism, proton-transporting V-type ATPase, V1domain 566 1AXg8275.t1 2363 1BXg5365.t1 None None 0.02 0 4.5 4.5 0.02567 1AXg1909.t1 2364 1BXg6126.t1 None peptidase activity 0.02 0 4.5 4.50.03 568 1AXg4752.t1 2365 1BXg2001.t1 AMPK signaling pathway,ascospore-type prospore 0 0.02 −4.5 4.5 0.03 Pancreatic secretion,assembly, autophagy, cytosol, RAB8A, MEL exocytosis, Golgi to plasmamembrane transport, GTP binding, GTPase activity, incipient cellular budsite, intracellular protein transport, membrane, membrane addition atsite of cytokinesis, metabolic process, nucleocytoplasmic transport,nucleus, small GTPase mediated signal transduction, transport vesicle,vesicle fusion 569 1AXg3765.t1 2366 1BXg2666.t1 None catalytic activity,integral 0 0.02 −4.4 4.4 0.02 component of membrane, metabolic process570 1AXg2891.t1 2367 1BXg10882.t1 None carboxypeptidase activity, 0 0.02−4.4 4.4 0.03 metallocarboxypeptidase activity, proteolysis, zinc ionbinding 478 1AXg10805.t1 2368 1BXg9667.t1 None carbohydrate metabolicprocess, 0.98 0.05 4.4 4.4 0.04 cellulose binding, extracellular region,glucosylceramidase activity, sphingolipid metabolic process 5711AXg5891.t1 2369 1BXg10979.t1 E5.2.1.8 apoptotic process, cytosol, 00.02 −4.4 4.4 0.05 mitochondrion, nucleus, peptidyl-prolyl cis-transisomerase activity, protein folding, protein peptidyl-prolylisomerization 572 1AXg10065.t1 2370 1BXg2722.t1 None None 0.36 0.02 4.34.3 0.02 573 1AXg19725.t1 2371 1BXg7679.t1 Ribosome, RP-L7e, RPL7ribosome 0 0.02 −4.3 4.3 0.02 574 1AXg20723.t1 2372 1BXg2050.t1 Noneintegral component of 0 0.02 −4.3 4.3 0.02 membrane, transmembranetransport, transmembrane transporter activity 575 1AXg21175.t1 23731BXg6238.t1 Ribosome, RP-L13Ae, large ribosomal subunit, 0 0.02 −4.3 4.30.04 RPL13A structural constituent of ribosome, translation 5761AXg2292.t1 2374 1BXg10711.t1 ARN integral component of 0 0.02 −4.2 4.20.01 membrane, transmembrane transport 577 1AXg1391.t1 2375 1BXg3917.t1None cytosol, nucleus, proteolysis, 0 0.02 −4.2 4.2 0.05 serine-typepeptidase activity 578 1AXg8174.t1 2376 1BXg7986.t1 None catalyticactivity, cell, cell 0 0.02 −4.1 4.1 0.03 redox homeostasis, glycerolether metabolic process, integral component of membrane, membrane,oxidation-reduction process, protein disulfide oxidoreductase activity,single-organism cellular process, single- organism metabolic process,translation 480 1AXg3149.t1 2377 1BXg4998.t1 E3.2.1.67, Pentose andcarbohydrate metabolic process, 0.55 0.03 4 4 0.02 glucuronateinterconversions, cell wall organization, Starch and sucroseextracellular region, hydrolase metabolism activity, acting on glycosylbonds, polygalacturonase activity 579 1AXg4184.t1 2378 1BXg1792.t1 Noneintegral component of 0.02 0 4 4 0.03 membrane 580 1AXg5751.t1 23791BXg7894.t1 Carbohydrate digestion and alpha-amylase activity, 0.02 0 44 0.03 absorption, E3.2.1.1, amyA, carbohydrate metabolic process, malS,Starch and sucrose cation binding, oxidation- metabolism reductionprocess, oxidoreductase activity, starch binding 581 1AXg10745.t1 23801BXg11993.t1 None None 0.02 0 4 4 0.03 582 1AXg8977.t1 2381 1BXg11388.t1TC.POT integral component of 0 0.02 −4 4 0.04 membrane, oligopeptidetransport, transporter activity 583 1AXg2503.t1 2382 1BXg3531.t1 Aminosugar and nucleotide carbohydrate metabolic process, 0 0.02 −4 4 0.05sugar metabolism, Galactose intramolecular transferase metabolism,Glycolysis/ activity, phosphotransferases, Gluconeogenesis, Pentosemagnesium ion binding, phosphate pathway, nucleus pgm, Purinemetabolism, Starch and sucrose metabolism, Streptomycin biosynthesis 5841AXg3358.t1 2383 1BXg4769.t1 None None 0 0.07 −3.9 3.9 0 585 1AXg8317.t12384 1BXg5117.t1 None None 0 0.07 −3.9 3.9 0 586 1AXg4278.t1 23851BXg1931.t1 AFG1, LACE1, zapE ATP binding, cellular response 0 0.01 −3.93.9 0.02 to oxidative stress, misfolded or incompletely synthesizedprotein catabolic process, mitochondrial inner membrane, protein importinto peroxisome matrix 587 1AXg11050.t1 2386 1BXg2887.t1 Noneproteolysis, serine-type 0.06 0 3.9 3.9 0.03 carboxypeptidase activity588 1AXg8247.t1 2387 1BXg10032.t1 Biosynthesis of amino acids, canonicalglycolysis, 0.01 0.09 −3.9 3.9 0.04 Carbon fixation in gluconeogenesis,photosynthetic organisms, mitochondrion, nucleus, Carbon metabolism,Fructose pentose-phosphate shunt, and mannose metabolism,triose-phosphate isomerase Glycolysis/Gluconeogenesis, activity Inositolphosphate metabolism, TPI, tpiA 589 1AXg5531.t1 2388 1BXg11344.t1E3.2.1.6 carbohydrate metabolic process, 0 0.01 −3.8 3.8 0.02 hydrolaseactivity, hydrolyzing O-glycosyl compounds 590 1AXg9521.t1 23891BXg6591.t1 None cellular aromatic compound 0 0.01 −3.8 3.8 0.02metabolic process, ferric iron binding, integral component of membrane,oxidation-reduction process, oxidoreductase activity, acting on singledonors with incorporation of molecular oxygen, incorporation of twoatoms of oxygen 591 1AXg11377.t1 2390 1BXg307.t1 XEG carbohydratemetabolic process, 0 0.01 −3.8 3.8 0.03 hydrolase activity, acting onglycosyl bonds, hydrolase activity, hydrolyzing O-glycosyl compounds 5921AXg7658.t1 2391 1BXg7553.t1 Cysteine and methionine cellular responseto oxidative 0 0.01 −3.8 3.8 0.04 metabolism, E1.8.4.14 stress,cytoplasm, methionine- R-sulfoxide reductase activity,oxidation-reduction process 593 1AXg1255.t1 2392 None None 0.14 0.01 3.83.8 0.04 594 1AXg11060.t1 2393 1BXg1582.t1 None integral component of 00.01 −3.7 3.7 0.02 membrane, transmembrane transport 595 1AXg6907.t12394 1BXg8642.t1 None None 0.01 0 3.7 3.7 0.02 596 1AXg1976.t1 23951BXg6237.t1 None intracellular ribonucleoprotein 0.01 0 3.7 3.7 0.02complex 597 1AXg10216.t1 2396 1BXg11971.t1 None cell redox homeostasis,cellular 0 0.01 −3.7 3.7 0.02 response to oxidative stress, glutathioneperoxidase activity, mitochondrion, oxidation- reduction process,response to cadmium ion, thioredoxin peroxidase activity 598 1AXg8251.t12397 1BXg10028.t1 None hydrolase activity, acting on 0 0.01 −3.7 3.70.03 carbon-nitrogen (but not peptide) bonds, metabolic process 5991AXg6457.t1 2398 1BXg5328.t1 None integral component of 0 0.01 −3.7 3.70.03 membrane, membrane, transmembrane transport 600 1AXg11201.t1 23991BXg8976.t1 None None 0.2 0.01 3.7 3.7 0.05 601 1AXg21445.t1 24001BXg11743.t1 Ribosome, RP-SAe, RPSA cytosolic small ribosomal 0 0.01−3.6 3.6 0.03 subunit, ribosomal small subunits assembly, structuralconstituent of ribosome, translation 602 1AXg12611.t1 2401 1BXg3489.t1None acid phosphatase activity, 0.05 0 3.6 3.6 0.04 dephosphorylation,integral component of membrane 603 1AXg81.t1 2402 1BXg10975.t1 None None0 0.01 −3.6 3.6 0.04 604 1AXg3188.t1 2403 1BXg9954.t1 None None 0.01 03.5 3.5 0.02 605 1AXg7341.t1 2404 1BXg10389.t1 None None 0 0.01 −3.5 3.50.03 606 1AXg8340.t1 2405 1BXg5141.t1 Oxidative phosphorylation, aerobicrespiration, cellular 0 0.01 −3.5 3.5 0.04 ppa metabolic process,cytoplasm, inorganic diphosphatase activity, magnesium ion binding,mitochondrion, phosphate-containing compound metabolic process 6071AXg6585.t1 2406 1BXg10114.t1 FTR, efeU high-affinity iron ion 0 0.01−3.5 3.5 0.04 transmembrane transport, high- affinity iron permeasecomplex, integral component of membrane, iron ion transmembranetransporter activity, metabolic process, transferase activity 6081AXg1785.t1 2407 1BXg1175.t1 Amino sugar and nucleotidebeta-N-acetylhexosaminidase 0.02 0.17 −3.4 3.4 0.01 sugar metabolism,activity, carbohydrate metabolic Glycosaminoglycan process degradation,Glycosphingolipid biosynthesis - ganglio series, Glycosphingolipidbiosynthesis - globo series, HEXA_B, Lysosome, Other glycan degradation609 1AXg2827.t1 2408 1BXg9091.t1 map aminopeptidase activity, 0.01 0 3.43.4 0.02 fumagillin biosynthetic process, metal ion binding,metalloexopeptidase activity, proteolysis 610 1AXg3285.t1 24091BXg8264.t1 None cell part 0 0.01 −3.4 3.4 0.02 611 1AXg7102.t1 24101BXg5569.t1 None None 0 0.01 −3.4 3.4 0.02 612 1AXg9751.t1 24111BXg1036.t1 E3.6.3.6, Oxidative ATP binding, ATP biosynthetic 0 0.01−3.4 3.4 0.02 phosphorylation process, hydrogen ion transmembranetransport, hydrogen-exporting ATPase activity, phosphorylativemechanism, integral component of membrane, metal ion binding 6131AXg3114.t1 2412 1BXg11816.t1 None hydrolase activity, positive 0 0.01−3.4 3.4 0.03 regulation of translation, positive regulation oftranslational elongation, positive regulation of translationaltermination, ribosome binding, RNA binding, translation elongationfactor activity, translational elongation, translational frameshifting614 1AXg2047.t1 2413 1BXg2549.t1 None carbohydrate metabolic process,0.05 0.46 −3.3 3.3 0.02 cell wall, cell wall organization, hydrolaseactivity, hydrolyzing O-glycosyl compounds, transferase activity 6151AXg524.t1 2414 1BXg8254.t1 None integral component of 0 0.01 −3.3 3.30.02 membrane, transmembrane transport 616 1AXg5090.t1 2415 1BXg2954.t1SNARE interactions in integral component of 0 0.01 −3.3 3.3 0.02vesicular transport, membrane, vesicle-mediated STX1B_2_3, Synaptictransport vesicle cycle 617 1AXg6524.t1 2416 1BXg2065.t1 Alzheimer′sdisease, Cardiac 2 iron, 2 sulfur cluster binding, 0 0.01 −3.3 3.3 0.03muscle contraction, aerobic respiration, hydrogen Huntington′s disease,Non- ion transmembrane transport, alcoholic fatty liver disease metalion binding, (NAFLD), Oxidative mitochondrial electron phosphorylation,Parkinson′s transport, ubiquinol to disease, Two-component cytochrome c,mitochondrial system, UQCRFS1, RIP1, respiratory chain complex III, petAubiquinol-cytochrome-c reductase activity 618 1AXg9485.t1 24171BXg5765.t1 None ATP binding, ATPase activity, 0.01 0 3.3 3.3 0.04endoplasmic reticulum, integral component of membrane, metabolic process619 1AXg3460.t1 2418 1BXg4685.t1 Biosynthesis of amino acids, ATPphosphoribosyltransferase 0 0.05 −3.2 3.2 0.01 hisG, Histidinemetabolism activity, cytosol, histidine biosynthetic process, magnesiumion binding 620 1AXg3259.t1 2419 1BXg8229.t1 PMPCB, MAS1 metal ionbinding, 0 0.01 −3.2 3.2 0.02 metalloendopeptidase activity,mitochondrial processing peptidase complex, protein processing involvedin protein targeting to mitochondrion 621 1AXg7607.t1 2420 1BXg7629.t1None integral component of 0 0.01 −3.2 3.2 0.02 membrane 622 1AXg3160.t12421 1BXg1334.t1 PHO84 inorganic phosphate 0.01 0.1 −3.1 3.1 0transmembrane transporter activity, integral component of membrane,phosphate ion transport, transmembrane transport 623 1AXg459.t1 24221BXg8019.t1 E3.2.1.101 catalytic activity, membrane 0.03 0 3.1 3.1 0.01624 1AXg11134.t1 2423 1BXg6417.t1 None cytoplasmic part, 0 0.01 −3.1 3.10.02 endomembrane system, integral component of membrane, intracellularmembrane- bounded organelle, transmembrane transport 625 1AXg14833.t12424 1BXg6900.t1 Calcium signaling pathway, ADP transport, ATP:ADP 00.01 −3.1 3.1 0.02 cGMP-PKG signaling antiporter activity, DNA repair,pathway, HTLV-I infection, integral component of Huntington′s disease,membrane, kinetochore Parkinson′s disease, assembly, mitochondrial ATPSLC25A4S, ANT transmembrane transport, mitochondrial inner membrane 6261AXg2308.t1 2425 1BXg10725.t1 None NAD(P)+ transhydrogenase 0 0.01 −3.13.1 0.02 activity, single-organism process 627 1AXg7369.t1 24261BXg10420.t1 SLC25A23S 3′-phospho-5′-adenylyl sulfate 0 0.01 −3.1 3.10.04 transmembrane transport, 3′- phosphoadenosine 5′- phosphosulfatetransmembrane transporter activity, 5′-adenylyl sulfate transmembranetransport, 5′-adenylyl sulfate transmembrane transporter activity,integral component of membrane, intracellular ribonucleoprotein complex,mitochondrion, ribosome, structural constituent of ribosome, translation628 1AXg1858.t1 2427 1BXg1886.t1 None intracellular part 0 0.01 −3.1 3.10.05 629 1AXg8166.t1 2428 1BXg7974.t1 None membrane 0 0.01 −3.1 3.1 0.05630 1AXg2960.t1 2429 1BXg5945.t1 None None 0.13 0.02 3 3 0.01 6311AXg4213.t1 2430 1BXg1766.t1 None membrane 0 0.01 −3 3 0.02 6321AXg4083.t1 2431 1BXg3283.t1 None integral component of 0 0.01 −3 3 0.02membrane, plasma membrane, transport 633 1AXg3175.t1 2432 1BXg2690.t1E3.2.1.- carbohydrate metabolic process, 0.01 0 3 3 0.03 cellulosebinding, extracellular region, hydrolase activity, hydrolyzingO-glycosyl compounds 634 1AXg11576.t1 2433 1BXg11481.t1 None flavinadenine dinucleotidc 0 0.01 −3 3 0.04 binding, oxidation-reductionprocess, oxidoreductase activity, acting on CH—OH group of donors 6351AXg511.t1 2434 1BXg3351.t1 None oxidoreductase activity 0.1 0.01 2.92.9 0.01 636 1AXg8734.t1 2435 1BXg11562.t1 None chitin binding, chitincatabolic 0 0.01 −2.9 2.9 0.02 process, chitinase activity,extracellular region, pathogenesis, polysaccharide catabolic process 6371AXg6748.t1 2436 1BXg4362.t1 E3.2.1.58, Starch and endoplasmicreticulum, fungal- 0 0.01 −2.9 2.9 0.05 sucrose metabolism type cellwall beta-glucan biosynthetic process, glucan endo-1,6-beta-glucosidaseactivity, integral component of membrane, regulation of cell shape 6381AXg10079.t1 2437 1BXg2701.t1 HSPA5, BIP, Prion diseases, ′de novo′posttranslational 0 0.01 −2.8 2.8 0.02 Protein export, Protein proteinfolding, ATP binding, processing in endoplasmic ATPase activity,ER-associated reticulum, Thyroid hormone ubiquitin-dependent proteinsynthesis catabolic process, Golgi apparatus, karyogamy involved inconjugation with cellular fusion, luminal surveillance complex, nuclearmembrane, posttranslational protein targeting to membrane,translocation, response to unfolded protein, SRP- dependentcotranslational protein targeting to membrane, translocation, unfoldedprotein binding 639 1AXg10129.t1 2438 1BXg8487.t1 None None 0 0.01 −2.82.8 0.05 482 1AXg10578.t1 2439 1BXg12089.t1 None aspartic-typeendopeptidase 0.53 0.08 2.7 2.7 0.02 activity, proteolysis 6401AXg12554.t1 2440 1BXg3576.t1 Ribosome, RP-S13e, RPS13 cytoplasmictranslation, 0.01 0 2.7 2.7 0.02 cytosolic small ribosomal subunit,maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8SrRNA, LSU-rRNA), mycelium development, small ribosomal subunit rRNAbinding, structural constituent of ribosome 641 1AXg15417.t1 24411BXg6538.t1 Protein processing in acid-amino acid ligase activity, 0.010 2.7 2.7 0.02 endoplasmic reticulum, APC-Cdc20 complex activity,UBE2D_E, UBC4, UBC5, ATP binding, cytosol, nuclear Ubiquitin mediatedSCF ubiquitin ligase complex, proteolysis positive regulation of mitoticmetaphase/anaphase transition, protein processing, proteinubiquitination involved in ubiquitin-dependent protein catabolicprocess, SCF- dependent proteasomal ubiquitin-dependent proteincatabolic process, ubiquitin conjugating enzyme activity 642 1AXg4473.t12442 1BXg9969.t1 SLC39A1_2_3, ZIP1_2_3 cellular response to zinc ion0.01 0.06 −2.6 2.6 0.01 starvation, endoplasmic reticulum, high-affinityzinc II ion transport, high-affinity zinc uptake transmembranetransporter activity, integral component of plasma membrane, regulationof transcription from RNA polymerase II promoter in response to iron ionstarvation 643 1AXg13171.t1 2443 1BXg1289.t1 E3.2.1.28, treA, treF,Starch alpha, alpha-trehalase activity, 0.03 0 2.6 2.6 0.02 and sucrosemetabolism trehalose metabolic process 644 1AXg4544.t1 2444 1BXg4073.t1Ribosome, RP-L9e, RPL9 ribosome, rRNA binding, 0.01 0 2.6 2.6 0.02structural constituent of ribosome, translation 645 1AXg13885.t1 24451BXg12241.t1 Ether lipid metabolism, hydrolase activity, acting on 0.060.36 −2.5 2.5 0 Glycerophospholipid ester bonds, metabolic processmetabolism, Inositol phosphate metabolism, plcC, Thyroid hormonesignaling pathway 646 1AXg8079.t1 2446 1BXg7852.t1 None hydrolaseactivity, metabolic 0.01 0.05 −2.5 2.5 0.02 process 647 1AXg1002.t1 24471BXg8071.t1 Alzheimer′s disease, ATP synthesis coupled proton 0 0 2.42.4 0.02 ATPeF0D, ATP5H, ATP7, transport, mitochondrial proton-Huntington′s disease, transporting ATP synthase, Oxidativephosphorylation, stator stalk, protein complex Parkinson′s diseaseassembly, proton-transporting ATP synthase activity, rotationalmechanism, proton- transporting ATPase activity, rotational mechanism648 1AXg14938.t1 2448 1BXg3779.t1 ARF1, Endocytosis, Golgi apparatus,GTP binding, 0 0 2.4 2.4 0.02 Legionellosis, Vibrio hydrolase activity,intracellular cholerae infection protein transport, metabolic process,small GTPase mediated signal transduction 649 1AXg2148.t1 24491BXg11881.t1 Adherens junction, ascospore formation, cell 0 0 2.4 2.40.02 Amyotrophic lateral sclerosis division, conidium formation, (ALS),Axon guidance, B developmental pigmentation, cell receptor signalingendomembrane system, fungal- pathway, Bacterial invasion type vacuolemembrane, GTP of epithelial cells, cAMP binding, GTPase activity,signaling pathway, intracellular protein transport, Chemokine signalingmetabolic process, pathway, Choline nucleocytoplasmic transport,metabolism in cancer, pathogenesis, plasma Colorectal cancer, Epithelialmembrane, small GTPase cell signaling in mediated signal transductionHelicobacter pylori infection, Fc epsilon RI signaling pathway, Fc gammaR-mediated phagocytosis, Focal adhesion, Leukocyte transendothelialmigration, MAPK signaling pathway, Natural killer cell mediatedcytotoxicity, Neurotrophin signaling pathway, Non- alcoholic fatty liverdisease (NAFLD), Osteoclast differentiation, Pancreatic cancer,Pancreatic secretion, Pathways in cancer, Phagosome, PI3K-Akt signalingpathway, Proteoglycans in cancer, RAC1, Rap1 signaling pathway, Rassignaling pathway, Regulation of actin cytoskeleton, Renal cellcarcinoma, Salmonella infection, Shigellosis, Sphingolipid signalingpathway, Toll-like receptor signaling pathway, VEGF signaling pathway,Viral carcinogenesis, Viral myocarditis, Wnt signaling pathway 6501AXg7481.t1 2450 1BXg6855.t1 None integral component of 0 0 −2.4 2.40.02 membrane, membrane, transmembrane transport 651 1AXg9624.t1 24511BXg7238.t1 None anchored component of 0.01 0.06 −2.4 2.4 0.03 membrane,carbohydrate metabolic process, fungal-type cell wall, hydrolaseactivity, plasma membrane, transferase activity 652 1AXg7771.t1 24521BXg7838.t1 None proteolysis, serine-type 0.11 0.02 2.4 2.4 0.03endopepetidase activity 653 1AXg1042.t1 2453 1BXg8113.t1 None membrane0.02 0.1 −2.3 2.3 0.01 654 1AXg10247.t1 2454 1BXg3602.t1 None None 00.02 −2.3 2.3 0.02 493 1AXg12742.t1 2455 1BXg2905.t1 None hydrolaseactivity, hydrolyzing 0.21 1.08 −2.3 2.3 0.02 O-glycosyl compounds,mycelium development, organic substance metabolic process 6551AXg15299.t1 2456 1BXg10457.t1 K07975 cellular bud, cytosol, 0 0 2.3 2.30.02 establishment or maintenance of actin cytoskeleton polarity,establishment or maintenance of cell polarity regulating cell shape, GTPbinding, GTPase activity, membrane, metabolic process, microtubulecytoskeleton organization, nucleus, positive regulation of exocytosis,positive regulation of formin-nucleated actin cable assembly, proteintransport, regulation of cell separation after cytokinesis, small GTPasemediated signal transduction 656 1AXg16181.t1 2457 1BXg12075.t1E3.2.1.101 carbohydrate catabolic process, 0 0 −2.3 2.3 0.02 hydrolaseactivity, mannan endo-1,6-alpha- mannosidase activity 657 1AXg4821.t12458 1BXg705.t1 None None 0.19 0.95 −2.3 2.3 0.02 658 1AXg4879.t1 24591BXg4499.t1 Amoebiasis, Endocytosis, cytosol, fungal-type vacuole 0 02.3 2.3 0.02 Phagosome, RAB7A, membrane, GTP binding, Salmonellainfection, GTPase activity, intracellular Tuberculosis proteintransport, mitochondrial outer membrane, nucleocytoplasmic transport,piecemeal microautophagy of nucleus, plasma membrane, positiveregulation of vacuole fusion, non-autophagic, protein localization tovacuole, regulation of endocytosis, retrograde transport, endosome toGolgi, small GTPase mediated signal transduction, vacuolaracidification, vacuole inheritance, vesicle fusion with vacuole 6591AXg5864.t1 2460 1BXg10898.t1 APRT, apt, Purine adenine 0 0 2.3 2.3 0.02metabolism phosphoribosyltransferase activity, adenine salvage, AMPsalvage, cytosol 660 1AXg8547.t1 2461 1BXg10270.t1 Ribosome, RP-L10Ae,large ribosomal subunit, RNA 0 0 2.3 2.3 0.02 RPL10A binding, structuralconstituent of ribosome, translation 661 1AXg2128.t1 2462 1BXg11919.t1None carboxypeptidase activity, 0.02 0 2.2 2.2 0.01 membrane 6621AXg7452.t1 2463 1BXg6885.t1 cdd, CDA, Drug cytidine deaminase activity,0.09 0.02 2.2 2.2 0.03 metabolism - other cytidine deamination, enzymes,Pyrimidine cytoplasm, zinc ion binding metabolism 663 1AXg4563.t1 24641BXg4094.t1 ribH, RIB4, Riboflavin 6,7-dimethyl-8-ribityllumazine 0.020.08 −2.2 2.2 0.04 metabolism synthase activity, mitochondrialintermembrane space, riboflavin binding, riboflavin biosyntheticprocess, riboflavin synthase complex, transferase activity 6641AXg10907.t1 2465 1BXg5915.t1 None cytosol, GU repeat RNA 0 0 2.1 2.10.02 binding, intracellular part, microsatellite binding, nucleus, RNAbinding, sequence- specific DKA binding, single- stranded telomeric DNAbinding 665 1AXg4299.t1 2466 1BXg1953.t1 Acute myeloid leukemia, GTPbinding, GTPase activity, 0 0 2.1 2.1 0.02 Alcoholism, Aldosterone-intracellular, intracellular regulated sodium protein transport,metabolic reabsorption, Axon guidance, process, nucleocyloplasmic B cellreceptor signaling transport, plasma membrane, pathway, Bladder cancer,small GTPase mediated signal Central carbon metabolism transduction incancer, Chemokine signaling pathway, Choline metabolism in cancer,Cholinergic synapse, Chronic myeloid leukemia, Colorectal cancer, Dorso-ventral axis formation, Endometrial cancer, ErbB signaling pathway,Estrogen signaling pathway, Fc epsilon RI signaling pathway, FoxOsignaling pathway, Gap junction, Glioma, GnRH signaling pathway,Hepatitis B, Hepatitis C, HTLV-I infection, Insulin signaling pathway,KRAS, KRAS2, Long-term depression, Long- term potentiation, MAPKsignaling pathway, MAPK signaling pathway - fly, Melanogenesis,Melanoma, MicroRNAs in cancer, Natural killer cell mediatedcytotoxicity, Neurotrophin signaling pathway, Non- small cell lungcancer, Oxytocin signaling pathway, Pancreatic cancer, Pathways incancer, PI3K-Akt signaling pathway, Progesterone-mediated oocytematuration, Prolactin signaling pathway, Prostate cancer, Proteoglycansin cancer, Rap1 signaling pathway, Ras signaling pathway, Regulation ofactin cytoskeleton, Renal cell carcinoma, Serotonergic synapse,Signaling pathways regulating pluripotency of stem cells, Sphingolipidsignaling pathway, T cell receptor signaling pathway, Thyroid cancer,Thyroid hormone signaling pathway, Tight junction, VEGF signalingpathway, Viral carcinogenesis 666 1AXg9261.t1 2467 1BXg10439.t1E3.4.21.48 dibasic protein processing, 0.01 0.03 −2.1 2.1 0.02serine-type endopeptidase activity 667 1AXg9193.t1 2468 1BXg8761.t1 Nonechitosanase activity, 0.17 0.04 2.1 2.1 0.02 extracellular region,polysaccharide catabolic process 668 1AXg4669.t1 2469 1BXg10567.t1 Nonehydrolase activity, acting on 0 0 −2.1 2.1 0.03 carbon-nitrogen (but notpeptide) bonds, integral component of membrane, metabolic process 6691AXg19989.t1 2470 1BXg9824.t1 glgB, Starch and sucrose 1,4-alpha-glucanbranching 0 0 −2.1 2.1 0.05 metabolism enzyme activity, ATP binding, ATPhydrolysis coupled proton transport, ATP synthesis coupled protontransport, cation binding, cytoplasm, glycogen biosynthetic process,hydrolase activity, hydrolyzing O-gyclosyl compounds,proton-transporting ATP synthase activity, rotational mechanism,proton-transporting ATP synthase complex, catalytic core F(1) 6701AXg2882.t1 2471 1BXg10869.t1 Glycerophospholipid lysophospholipaseactivity, 0.06 0.01 2 2 0 metabolism, PLB phospholipid catabolic process671 1AXg5521.t1 2472 1BXg1647.t1 Ribosome, RP-S4e, RPS4 ribosome, rRNAbinding, 0 0 2 2 0.02 structural constituent of ribosome, translation672 1AXg2908.t1 2473 1BXg6003.t1 AXL2 None 0.02 0 2 2 0.02 6731AXg6960.t1 2474 1BXg9737.t1 None aspartic-type endopeptidase 0.1 0.03 22 0.05 activity, proteolysis This table describes the differentialprotein expression between pairs of orthologous proteins from a genus,where one member of the pair has a beneficial effect on plant growth andthe other has a neutral effect. “A.mean” represents the averagenormalized spectral counts between biological replicates of thebeneficial member of the pair. “B.mean” represents the averagenormalized spectral counts between biological replicates of the neutralmember of the pair. “Fold change” represents the fold change differencbetween the two organisms. “FDR q-value” represents the false discoveryrate corrected q-value.

A total of 892 proteins were detected across all Acremonium samples withtwo or more unique peptides at the false discovery rates indicatedabove.

SYM15774 Secreted Proteomic Analysis

TABLE 702 25 most abundant proteins secreted by SYM15774; “MedianAbundance” represents the median value across three biologicalreplicates in units of spectra per hundred spectra SEQ Median ID ProteinID Abundance GO Terms KEGG Terms 4510 3AXg6236.t1 1.09684 GO:0005576:extracellular region none 4511 3AXg9048.t1 1.031017 GO:0000287:magnesium ion none binding; GO:0006400: tRNA modification; GO:0008193:tRNA guanylyltransferase activity; GO:0016787: hydrolase activity 45123AXg678.t1 0.62687 GO:0016787: hydrolase activity none 4513 3AXg934.t10.558301 GO:0003735: structural constituent KEGG Orthology: K02927: RP-of ribosome; GO:0005840: ribosome; L40e, RPL40: large subunitGO:0006412: translation ribosomal protein L40e; KEGG PATHWAY: ko03010:Ribosome: 4514 3AXg7460.t1 0.527389 GO:0005886: plasma membrane; noneGO:0005975: carbohydrate metabolic process; GO:0016021: integralcomponent of membrane; GO:0016740: transferase activity; GO:0016787:hydrolase activity; GO:0031225: anchored component of membrane 45153AXg10862.t1 0.523646 GO:0004650: polygalacturonase KEGG Orthology:K01213: activity; GO:0005576: extracellular E3.2.1.67: galacturan1,4-alpha- region; GO:0005975: carbohydrate galacturonidase[EC:3.2.1.67]; metabolic process; GO:0071555: cell KEGG PATHWAY:ko00040: wall organization Pentose and glucuronate interconversions:;KEGG PATHWAY: ko00500: Starch and sucrose metabolism: 4516 3AXg8590.t10.400556 GO:0008061: chitin binding KEGG Orthology: K00799: GST, gst:glutathione S-transferase [EC:2.5.1.18]; KEGG PATHWAY: ko00480:Glutathione metabolism:; KEGG PATHWAY: ko00980: Metabolism ofxenobiotics by cytochrome P450:; KEGG PATHWAY: ko00982: Drugmetabolism - cytochrome P450:; KEGG PATHWAY: ko05204: Chemicalcarcinogenesis: It has been estimated that exposure to environmentalchemical carcinogens may contribute significantly to the causation of asizable fraction, perhaps a majority, of human cancers. Humancarcinogens act through a variety of genotoxic and non-genotoxicmechanisms. Genotoxic carcinogens can attack biological macromoleculessuch as DNA and RNA either directly or indirectly through metabolism,resulting in the formation of adducts with these macromolecules. If DNAadducts escape cellular repair mechanisms and persist, they may lead tomiscoding, resulting in permanent mutations. Non-genotoxic carcinogensact by the mechanisms such as induction of inflammation,immunosuppression, formation of reactive oxygen species, activation ofreceptors, and epigenetic silencing. Together, these genotoxic and non-genotoxic mechanisms can alter signal- transduction pathways thatfinally result in hypermutability, genomic instability, loss ofproliferation control, and resistance to apoptosis - some of thecharacteristic features of cancer cells. 4517 3AXg5014.t1 0.375314GO:0004553: hydrolase activity, none hydrolyzing O-glycosyl compounds;GO:0005975: carbohydrate metabolic process 4518 3AXg2998.t1 0.374684GO:0016614: oxidoreductase none activity, acting on CH—OH group ofdonors; GO:0018130: heterocycle biosynthetic process; GO:0044550:secondary metabolite biosynthetic process; GO:0050660: flavin adeninedinucleotide binding; GO:0055114: oxidation-reduction process;GO:1901362: organic cyclic compound biosynthetic process 45193AXg4073.t1 0.311962 GO:0005975: carbohydrate none metabolic process;GO:0016787: hydrolase activity 4520 3AXg3348.t1 0.291735 GO:0006629:lipid metabolic none process; GO:0008081: phosphoric diester hydrolaseactivity 4521 3AXg1507.t1 0.287808 GO:0005886: plasma membrane; noneGO:0005975: carbohydrate metabolic process; GO:0016021: integralcomponent of membrane; GO:0016740: transferase activity; GO:0031225:anchored component of membrane 4522 3AXg2571.t1 0.275402 GO:0008152:metabolic process; none GO:0016787: hydrolase activity 4523 3AXg9962.t10.272744 GO:0016020: membrane none 4524 3AXg965.t1 0.254561 GO:0003723:RNA binding; none GO:0004521: endoribonuclease activity; GO:0016020:membrane; GO:0090502: RNA phosphodiester bond hydrolysis,endonucleolytic 4525 3AXg5987.tl 0.252385 GO:0004252: serine-type KEGGOrthology: K01279: TPP1, endopeptidase activity; GO:0005576: CLN2:tripeptidyl-peptidase I extracellular region; GO:0006508: [EC:3.4.14.9];KEGG PATHWAY: proteolysis; GO:0008240: ko04142: Lysosome: Lysosomes aretripeptidyl-peptidase activity membrane-delimited organelles in animalcells serving as the cell's main digestive compartment to which allsorts of macromolecules are delivered for degradation. They contain morethan 40 hydrolases in an acidic environment (pH of about 5). Aftersynthesis in the ER, lysosomal enzymes are decorated withmannose-6-phosphate residues, which are recognized by mannose-6-phosphate receptors in the trans- Golgi network. They are packagedinto clathrin-coated vesicles and are transported to late endosomes.Substances for digestion are acquired by the lysosomes via a series ofprocesses including endocytosis, phagocytosis, and autophagy. 45263AXg8810.t1 0.232932 GO:0004252: serine-type KEGG Orthology: K01279:TPP1, endopeptidase activity; CLN2: tripeptidyl-peptidase I GO:0006508:proteolysis [EC:3.4.14.9]; KEGG PATHWAY: ko04142: Lysosome: Lysosomesare membrane-delimited organelles in animal cells serving as the cell'smain digestive compartment to which all sorts of macromolecules aredelivered for degradation. They contain more than 40 hydrolases in anacidic environment (pH of about 5). After synthesis in the ER, lysosomalenzymes are decorated with mannose-6-phosphate residues, which arerecognized by mannose- 6-phosphate receptors in the trans- Golginetwork. They are packaged into clathrin-coated vesicles and aretransported to late endosomes. Substances for digestion are acquired bythe lysosomes via a series of processes including endocytosis,phagocytosis, and autophagy. 4527 3AXg1658.t1 0.226403 GO:0016614:oxidoreductase none activity, acting on CH—OH group of donors;GO:0050660: flavin adenine dinucleotide binding; GO:0055114:oxidation-reduction process 4528 3AXg2961.t1 0.220484 GO:0016491:oxidoreductase KEGG Orthology: K00505: TYR: activity; GO:0046872: metalion tyrosinase [EC:1.14.18.1]; KEGG binding; GO:0055114: oxidation-PATHWAY: ko00350: Tyrosine reduction process metabolism:; KEGG PATHWAY:ko00740: Riboflavin metabolism:; KEGG PATHWAY: ko00950: Isoquinolinealkaloid biosynthesis: Isoquinoline alkaloids are tyrosine- derivedplant alkaloids with an isoquinoline skeleton. Among thembenzylisoquinoline alkaloids form an important group with potentpharmacological activity, including analgesic compounds of morphine andcodeine, and anti-infective agents of berberine, palmatine, andmagnoflorine. Biosynthesis of isoquinoline alkaloids proceeds viadecarboxylation of tyrosine or DOPA to yield dopamine, which togetherwith 4-hydroxyphenylacetaldehyde, an aldehyde derived from tyrosine, isconverted to reticuline, an important precursor of variousbenzylisoquinoline alkaloids.; KEGG PATHWAY: ko00965: Betalainbiosynthesis: Betalains are water-soluble nitrogen-containing pigmentsthat are present in plants belonging to the order Caryophyllales (suchas cactus and amaranth families) and in higher fungi. They containbetalamic acid as the chromophore and are classified into two types:betacyanins and betaxanthins. Betacyanins contain a cyclo-DOPA residueand exhibit red/violet coloration, while betaxanthins contain differentamino acids or amino side chains and exhibit a yellow/orange coloration.The condensation of betalamic acid with amino acids (includingcyclo-DOPA or amines) in plants is a spontaneous reaction, not anenzyme-catalyzed reaction.; KEGG PATHWAY: ko04916: Melanogenesis:Cutaneous melanin pigment plays a critical role in camouflage, mimicry,social communication, and protection against harmful effects of solarradiation. Melanogenesis is under complex regulatory control by multipleagents. The most important positive regulator of melanogenesis is theMC1 receptor with its ligands melanocortic peptides. MC1R activates thecyclic AMP (cAMP) response-element binding protein (CREB). Increasedexpression of MITF and its activation by phosphorylation (P) stimulatethe transcription of tyrosinase (TYR), tyrosinase-related protein 1(TYRP1), and dopachrometautomerase (DCT), which produce melanin. Melaninsynthesis takes place within specialized intracellular organelles namedmelanosomes. Melanin- containing melanosomes then move from theperinuclear region to the dendrite tips and are transferred tokeratinocytes by a still not well- characterized mechanism. 45293AXg1976.t1 0.215291 GO:0004190: aspartic-type none endopeptidaseactivity; GO:0006508: proteolysis 4530 3AXg11128.t1 0.213705 GO:0005619:ascospore wall; none GO:0005783: endoplasmic reticulum; GO:0030476:ascospore wall assembly 4531 3AXg4486.t1 0.20608 GO:0008152: metabolicprocess; none GO:0016491: oxidoreductase activity; GO:0016787: hydrolaseactivity; GO:0046872: metal ion binding 4532 3AXg6046.t1 0.205931GO:0005975: carbohydrate none metabolic process; GO:0008810: cellulaseactivity 4533 3AXg3384.t1 0.192121 GO:0003824: catalytic activity none4534 3AXg2856.t1 0.187827 GO:0006508: proteolysis; none GO:0008236:serine-type peptidase activity

SYM15774 Versus SYM01331

TABLE 703 Differential secreted protein abundance between SYM15774 andSYM01331. SEQ ID A. SEQ ID B. A. B. Fold- FDR Beneficial protein Neutralprotein KEGG GO mean mean change q-value 4535 3AXg4278.t1 43373BXg6074.t1 E3.1.1.73 carboxylic ester 0.136 0 7.1 1.20E−02 hydrolaseactivity 4536 3AXg230.t1 4338 3BXg7469.t1 Axon guidance, actin corticalpatch, actin 0.041 0 5.4 1.20E−02 CFL, Fc gamma R- filament binding,actin mediated filament phagocytosis, depolymerization, actin Pertussis,filament severing, ATP Regulation of actin binding, cell division site,cytoskeleton cell tip, endocytosis, Golgi to plasma membrane proteintransport, integral component of membrane, protein refolding 45373AXg6225.t1 4339 3BXg6585.t1 Arginine and proline oxidation-reduction0.028 0 4.9 1.20E−02 metabolism, beta- process, oxidoreductase Alaninemetabolism, activity MPAO, PAO1 4538 3AXg8418.t1 4340 3BXg7838.t1 Noneflavin adenine 0.015 0 4 1.20E−02 dinucleotide binding,oxidation-reduction process, oxidoreductase activity, acting on CH—OHgroup of donors, phosphatidylinositol binding 4539 3AXg6767.t1 43413BXg3303.t1 None cell wall, cell wall 0.045 0.003 3.4 1.20E−02modification, hydrolase activity, acting on ester bonds, metabolicprocess, pectinesterase activity 4519 3AXg4073.t1 4342 3BXg8531.t1 Nonecarbohydrate metabolic 0.297 0.054 2.4 1.20E−02 process, hydrolaseactivity 4540 3AXg10237.t1 4343 3BXg1101.t1 XEG cellulase activity,0.127 0.03 2 1.20E−02 polysaccharide catabolic process 4541 3AXg6263.t14344 3BXg11238.t1 None None 0.204 0.049 2 1.20E−02 4542 3AXg5745.t1 43453BXg6273.t1 None fungal-type cell wall, 0.054 0.246 −2.2 1.20E−02fungal-type vacuole, metallopeptidase activity, proteolysis 45433AXg10791.t1 4346 3BXg9786.t1 bglX, Cyanoamino beta-glucosidaseactivity, 0.003 0.094 −4.4 1.20E−02 acid metabolism, carbohydratemetabolic Phenylpropanoid process biosynthesis, Starch and sucrosemetabolism 4544 3AXg7602.t1 4347 3BXg11695.t1 None aspartic-type 0 0.06−5.9 1.20E−02 endopeptidase activity, proteolysis 4545 3AXg8955.t1 43483BXg2490.t1 None None 0 0.132 −7.1 1.20E−02 4546 3AXg1865.t1 43493BXg9015.t1 None carbohydrate metabolic 0 0.145 −7.2 1.20E−02 process,hydrolase activity, hydrolyzing O-glycosyl compounds 4547 3AXg10977.t14350 3BXg7338.t1 None None 0.062 0.009 2.6 1.30E−02 4548 3AXg8244.t14351 3BXg2216.t1 E3.4.11.10 aminopeptidase activity, 0 0.003 −2 1.30E−02extracellular region, metal ion binding, nuclear pore, nucleocytoplasmictransport, proteolysis, structural constituent of nuclear pore 45493AXg2047.t1 4352 3BXg7322.t1 E3.1.1.73 hydrolase activity, 0 0.007 −31.30E−02 metabolic process 4550 3AXg2487.t1 4353 3BXg4014.t1 CTSA,Lysosome, proteolysis, serine-type 0 0.018 −4.2 1.30E−02Renin-angiotensin carboxy peptidase activity system 4551 3AXg3683.t14354 3BXg679.t1 None metallocarboxy peptidase 0 0.054 −5.8 1.30E−02activity, proteolysis, zinc ion binding 4552 3AXg5735.t1 43553BXg6263.t1 E3.4.21.48 dibasic protein processing, 0 0.07 −6.2 1.30E−02serine-type endopeptidase activity 4553 3AXg8371.t1 4356 3BXg11001.t1E4.2.2.10 extracellular region, pectin 0 0.171 −7.4 1.30E−02 lyaseactivity, polysaccharide catabolic process 4554 3AXg8798.t1 43573BXg4519.t1 None integral component of 0.041 0 5.4 1.40E−02 membrane,membrane, negative regulation of G2/M transition of mitotic cell cycle4555 3AXg3404.t1 4358 3BXg4400.t1 None choline dehydrogenase 0.169 0.0045 1.40E−02 activity, flavin adenine dinuclcotide binding,oxidation-reduction process 4556 3AXg3735.t1 4359 3BXg4453.t1 Nonemembrane 0.023 0 4.6 1.40E−02 4557 3AXg9146.t1 4360 3BXg2444.t1 Noneintegral component of 0.017 0 4.2 1.40E−02 membrane 4558 3AXg10088.t14361 3BXg1846.t1 None endonuclease activity, 0.075 0.009 3 1.40E−02exonuclease activity, integral component of membrane, nucleic acidphosphodiester bond hydrolysis 4559 3AXg10485.t1 4362 3BXg821.t1 Aminosugar and beta-N- 0.027 0.156 −2.5 1.40E−02 nucleotide sugaracetylglucosaminidase metabolism, activity, carbohydrateGlycosaminoglycan metabolic process, degradation, extracellular region,Glycosphingolipid N-acetylglucosamine biosynthesis - ganglio catabolicprocess series, Glycosphingolipid biosynthesis - globo series, HEXA_B,Lysosome, Other glycan degradation 4560 3AXg8514.t1 4363 3BXg7997.t1None choline dehydrogenase 0.074 0.551 −2.9 1.40E−02 activity, flavinadenine dinucleotide binding, oxidation-reduction process 45613AXg8930.t1 4364 3BXg5868.t1 None integral component of 0 0.008 −3.21.40E−02 membrane 4562 3AXg6329.t1 4365 3BXg3212.t1 E1.1.99.1, betA,alcohol metabolic process, 0.039 0.388 −3.3 1.40E−02 CHDH, Glycine,choline dehydrogenase serine and threonine activity, DNA binding,metabolism flavin adenine dinucleotide binding, metal ion binding,oxidation-reduction process, regulation of transcription, DNA-templated4563 3AXg9850.t1 4366 3BXg11232.t1 None catalytic activity, 0 0.023 −4.61.40E−02 chromatin silencing by small RNA, cytosol, endoplasmicreticulum unfolded protein response, nucleus 4564 3AXg1923.t1 43673BXg9196.t1 None hydrolase activity, 0 0.033 −5.1 1.40E−02 metabolicprocess 4565 3AXg6350.t1 4368 3BXg12502.t1 None proteolysis, serine-type0.015 0.67 −5.4 1.40E−02 peptidase activity 4566 3AXg9423.t1 43693BXg390.t1 Betalain biosynthesis, ion binding, metabolic 0 0.048 −5.61.40E−02 Isoquinoline alkaloid process, metal ion binding, biosynthesis,oxidation-reduction Melanogenesis, process, oxidoreductase Riboflavinactivity metabolism, TYR, Tyrosine metabolism 4567 3AXg5033.t1 43703BXg7845.t1 None cellular process, 0 0.098 −6.6 1.40E−02 membrane,metabolic process, single-organism process 4568 3AXg4645.t1 43713BXg8440.t1 None None 0 0.121 −6.9 1.40E−02 4527 3AXg1658.t1 43723BXg6710.t1 None flavin adenine 0.219 0 7.8 1.50E−02 dinucleotidebinding, oxidation-reduction process, oxidoreductase activity, acting onCH—OH group of donors 4569 3AXg8951.t1 4373 3BXg5043.t1 None hydrolaseactivity, acting 0.169 0 7.4 1.50E−02 on ester bonds, nucleic acidmetabolic process 4570 3AXg3962.t1 4374 3BXg2058.t1 None flavin adenine0.098 0 6.6 1.50E−02 dinucleotide binding, oxidation-reduction process,oxidoreductase activity, acting on CH—OH group of donors 45713AXg9121.t1 4375 3BXg2385.t1 E3.1.1.11, Pentose aspartyl esteraseactivity, 0.098 0 6.6 1.50E−02 and glucuronate cell wall, cell wallinterconversions, modification, extracellular Starch and sucrose region,pectin catabolic metabolism process, pectinesterase activity 45723AXg6312.t1 4376 3BXg3233.t1 None flavin adenine 0.059 0 5.9 1.50E−02dinucleotide binding, oxidation-reduction process, oxidoreductaseactivity, acting on CH—OH group of donors 4573 3AXg4810.t1 43773BXg1560.t1 E3.2.1.4, Starch and carbohydrate metabolic 0.049 0 5.71.50E−02 sucrose metabolism process, hydrolase activity, hydrolyzingO-glycosyl compounds 4574 3AXg1577.t1 4378 3BXg3030.t1 None hydrolaseactivity, 0.026 0 4.8 1.50E−02 metabolic process 4575 3AXg5120.t1 43793BXg10267.t1 EEF1B cytosol, eukaryotic 0.015 0 4 1.50E−02 translationelongation factor 1 complex, guanyl- nucleotide exchange factoractivity, maintenance of translational fidelity, negative regulation ofactin filament bundle assembly, positive regulation of GTPase activity,regulation of translational termination, translation elongation factoractivity, translational elongation 4576 3AXg2881.t1 4380 3BXg6431.t1msrA cellular response to 0.005 0 2.7 1.50E−02 hydrogen peroxide,cytosol, integral component of membrane, L-methionine biosyntheticprocess from methionine sulphoxide, L-methionine- (S)-S-oxide reductaseactivity, nucleus, oxidation-reduction process, peptide- methionine(S)-S-oxide reductase activity, protein repair 4577 3AXg2995.t1 43813BXg8638.t1 Influenza A, proteolysis, serine-type 0.071 0.01 2.71.50E−02 Neuroactive ligand-S endopeplidase activity receptorinteraction, Pancreatic secretion. Protein digestion and absorption, PRS4578 3AXg6701.t1 4382 3BXg7716.t1 Epstein-Barr vims cytosol, GTPbinding, 0.005 0 2.7 1.50E−02 infection, HTLV-I GTPase activity,infection, RAN, intracellular protein Ribosome biogenesis transport,membrane, in eukaryotes, RNA metabolic process, negative transportregulation of G2/M transition of mitotic cell cycle, nuclear pore,nucleocytoplasmic transport, small GTPase mediated signal transduction,stmctural constituent of nuclear pore 4579 3AXg10558.t1 43833BXg10095.t1 None None 0.005 0 2.6 1.50E−02 4580 3AXg9106.t1 43843BXg2351.t1 None cytoplasm 0.004 0 2.3 1.50E−02 4581 3AXg573.t1 43853BXg5286.t1 None aspartic-ripe 0.044 0.009 2.2 1.50E−02 endopeptidaseactivity, membrane, proteolysis 4525 3AXg5987.t1 4386 3BXg5319.t1Lysosome, TPP1, extracellular region, 0.261 0.057 2.2 1.50E−02 CLN2proteolysis, serine-type endopeptidase activity, tripeptidyl-peptidaseactivity 4582 3AXg10624.t1 4387 3BXg1050.t1 None choline dehydrogenase0.172 0.038 2.1 1.50E−02 activity, flavin adenine dinucleotide binding,integral component of membrane, oxidation- reduction process,transmembrane transport, transporter activity 4520 3AXg3348.t1 43883BXg5195.t1 None lipid metabolic process, 0.286 0.065 2.1 1.50E−02phosphoric diester hydrolase activity 4583 3AXg1574.t1 4389 3BXg791.t1None ATP binding, calmodulin 0.003 0 2 1.50E−02 binding, calmodulin-dependent protein kinase activity, cytosol, glucose catabolic process,manganese ion binding, negative regulation of calcineurin-NFAT signalingcascade, negative regulation of G2/M transition of mitotic cell cycle,negative regulation of transcription by transcription factorlocalization, negative regulation of transcription from RNA polymeraseII promoter, nucleus, phosphoglycerate mutase activity, proteinphosphorylation, regulation of nuclear division 4584 3AXg3704.t1 43903BXg4116.t1 None None 0.04 0.176 −2.1 1.50E−02 4585 3AXg7050.t1 43913BXg10636.t1 E3.2.1.101 catalytic activity, 0.014 0.064 −2.1 1.50E−02hydrolase activity 4586 3AXg11147.t1 4392 3BXg3457.t1 None defenseresponse to 0.01 0.065 −2.6 1.50E−02 bacterium, defense response tofungus, spore wall 4587 3AXg809.t1 4393 3BXg9916.t1 Noneacetyltransferase activity, 0 0.016 −4.1 1.50E−02 metabolic process,transferase activity 4588 3AXg1606.t1 4394 3BXg8171.t1 Betalainbiosynthesis, metabolic process, 0 0.038 −5.3 1.50E−02 Isoquinolinealkaloid N-acetyltransferase biosynthesis, activity, oxidation-Melanogenesis, reduction process, Riboflavin oxidoreductase activity,metabolism, TYR, transferase activity, Tyrosine metabolism transferringacyl groups 4589 3AXg5600.t1 4395 3BXg3227.t1 None None 0 0.086 −6.41.50E−02 4590 3AXg676.t1 4396 3BXg6951.t1 None None 0 0.319 −8.31.50E−02 4591 3AXg8215.t1 4397 3BXg2453.t1 None None 0.002 0.054 −4.31.70E−02 4592 3AXg4581.t1 4398 3BXg7071.t1 None hydrolase activity,0.076 0 6.3 1.80E−02 metabolic process 4593 3AXg3000.t1 4399 3BXg8643.t1None flavin adenine 0 0.042 −5.4 1.80E−02 dinucleotide binding,oxidation-reduction process, oxidoreductase activity, oxidoreductaseactivity, acting on CH—OH group of donors 4594 3AXg3931.t1 44003BXg1983.t1 None choline dehydrogenase 0.081 0 6.4 1.90E−02 activity,flavin adenine dinucleotide binding, oxidation-reduction process 45953AXg3946.t1 4401 3BXg1965.t1 None copper ion binding, 0.025 0 4.71.90E−02 oxidation-reduction process, oxidoreductase activity 45963AXg1894.t1 4402 3BXg9149.t1 None carbohydrate metabolic 0.016 0 42.00E−02 process, catalytic activity 4597 3AXg3686.t1 4403 3BXg689.t1None copper ion binding, 0.022 0.166 −2.9 2.00E−02 oxidation-reductionprocess, oxidoreductase activity 4598 3AXg9632.t1 4404 3BXg8688.t1 Nonebeta-N- 0 0.026 −4.8 2.00E−02 acetylhexosaminidase activity,carbohydrate metabolic process, integral component of membrane 45993AXg7875.t1 4405 3BXg925.t1 E3.1.3.25. IMPA, DNA binding, integral 00.031 −5 2.00E−02 suhB, Inositol component of membrane, phosphatephosphatidylinositol metabolism, phosphorylation Phosphatidylinositolsignaling system, Streptomycin biosynthesis 4600 3AXg6708.t1 44063BXg7541.t1 None membrane 0 0.036 −5.2 2.00E−02 4601 3AXg7523.t1 44073BXg2252.t1 None hydrolase activity, 0.029 0.007 2 2.10E−02 metabolicprocess 4602 3AXg9481.t1 4408 3BXg11985.t1 Amino sugar and carbohydratemetabolic 0.059 0.345 −2.5 2.10E−02 nucleotide sugar process, chitincatabolic metabolism, process, chitinase activity, E3.2.1.14 hydrolaseactivity, hydrolyzing O-glycosyl compounds, organic substance metabolicprocess, transferase activity, transferring glycosyl groups 46033AXg11091.t1 4409 3BXg13016.t1 None hydrolase activity, 0 0.007 −32.10E−02 hydrolyzing O-glycosyl compounds, metabolic process 46043AXg505.t1 4410 3BXg6843.t1 Amino sugar and ATP binding, 0 0.011 −3.62.10E−02 nucleotide sugar carbohydrate metabolism, Butirosinphosphorylation, cellular and neomycin glucose homeostasis,biosynthesis, cytosol, fructokinase Carbohydrate activity, fructose 6-digestion and phosphate metabolic absorption, Carbon process,glucokinase metabolism, Central activity, glucose 6- carbon metabolismin phosphate metabolic cancer, Fructose and process, glucose binding,mannose metabolism, glycolytic fermentation, Galactose glycolyticprocess, integral metabolism, component of membrane, Glycolysis/mannokinase activity, Gluconcogenesis, mannose metabolic HIF-1 signalingprocess, nuclear pore, pathway, HK, Insulin nucleocytoplasmic signalingpathway, transport, stmctural Starch and sucrose constituent of nuclearmetabolism, pore Streptomycin biosynthesis, Type II diabetes mellitus4605 3AXg671.t1 4411 3BXg6947.t1 None FMN binding, membrane, 0 0.015 −42.10E−02 oxidation-reduction process, oxidoreductase activity 46063AXg907.t1 4412 3BXg10711.t1 None None 0 0.048 −5.6 2.10E−02 46073AXg10465.t1 4413 3BXg14385.t1 E3.2.1.58, Starch and carbohydratemetabolic 0 0.235 −7.9 2.10E−02 sucrose metabolism process, hydrolaseactivity, hydrolyzing O-glycosyl compounds, integral component ofmembrane, transmembrane transport 4608 3AXg1008.t1 4414 3BXg9515.t1 Nonecholine dehydrogenase 0.068 0 6.1 2.20E−02 activity, flavin adeninedinucleotide binding, oxidation-reduction process 4609 3AXg2591.t1 44153BXg1833.t1 Betalain biosynthesis, metal ion binding, 0.126 0.023 2.42.20E−02 Isoquinoline alkaloid oxidation-reduction biosynthesis,process, oxidoreductase Melanogenesis, activity Riboflavin metabolism,TYR, Tyrosine metabolism 4610 3AXg4824.t1 4416 3BXg1527.t1 None None0.04 0 5.4 2.30E−02 4518 3AXg2998.t1 4417 3BXg8641.t1 None flavinadenine 0.37 0.038 3.3 2.30E−02 dinucleotide binding, heterocyclebiosynthetic process, organic cyclic compound biosynthetic process,oxidation- reduction process, oxidoreductase activity, acting on CH—OHgroup of donors, secondary metabolite biosynthetic process 46113AXg8768.t1 4418 3BXg429.t1 None hydrolase activity, 0.011 0.145 −3.62.30E−02 metabolic process 4612 3AXg11131.t1 4419 3BXg7381.t1 None None0 0.021 −4.5 2.30E−02 4613 3AXg3576.t1 4420 3BXg5515.t1 None None 00.063 −6 2.30E−02 4614 3AXg10565.t1 4421 3BXg10107.t1 Nonemetallocarboxy peptidase 0.016 0 4.1 2.50E−02 activity, proteolysis,zinc ion binding 4615 3AXg4536.t1 4422 3BXg3121.t1 Galactosecarbohydrate binding, 0.047 0.003 3.8 2.50E−02 metabolism, malZ,carbohydrate metabolic Starch and sucrose process, cellular process,metabolism glucosidase activity, hydrolase activity, hydrolyzingO-glycosyl compounds, integral component of membrane 4616 3AXg4165.t14423 3BXg6890.t1 bglX, Cyanoamino hydrolase activity, 0 0.01 −3.42.50E−02 acid metabolism, hydrolyzing O-glycosyl Phenylpropanoidcompounds, integral biosynthesis, Starch component of membrane, andsucrose polysaccharide catabolic metabolism process 4617 3AXg8420.t14424 3BXg7817.t1 yteR, yesR hydrolase activity, 0.007 0.147 −4.32.50E−02 metabolic process 4618 3AXg6634.t1 4425 3BXg567141 None acidphosphatase activity, 0.004 0.022 −2.1 2.60E−02 dephosphorylation 46193AXg5462.t1 4426 3BXg503.t1 None carbohydrate metabolic 0 0.03 −52.60E−02 process, hydrolase activity 4620 3AXg9660.t1 4427 3BXg10410.t1None copper ion binding, 0 0.032 −5 2.60E−02 oxidation-reductionprocess, oxidoreductase activity 4621 3AXg736.t1 4428 3BXg7066.t1 Nonebiosynthetic process, 0 0.062 −6 2.60E−02 carbohydrate metabolicprocess, cellulose binding, extracellular region, hydrolase activity,hydrolyzing O-glycosyl compounds, positive regulation of GTPaseactivity, pyridoxal phosphate binding, regulation of Rho protein signaltransduction, Rho guanyl-nucleotide exchange factor activity 46223AXg3304.t1 4429 3BXg5239.t1 None None 0.07 0 6.1 2.70E−02 45113AXg9048.t1 4430 3BXg11565.t1 None hydrolase activity, 0.974 0.079 3.62.70E−02 magnesium ion binding, tRNA guanylyltransferase activity, tRNAmodification 4623 3AXg2688.t1 4431 3BXg10864.t1 AMPK signaling6-phosphofructo-2-kinase 0.01 0 3.5 2.70E−02 pathway, Fructose andactivity, ATP binding, mannose metabolism, carbohydrate HIF-1 signalingphosphorylation, cytosol, pathway, PFKFB dephosphorylation, fructose2,6-bisphosphate metabolic process, fructose metabolic process,fructose-2,6-bisphosphate 2-phosphatase activity 4624 3AXg9670.t1 44323BXg5175.t1 CTSA, Lysosome, fungal-type vacuole, 0.005 0.046 −3 2.70E−02Renin-angiotensin nuclear pore, system nucleocytoplasmic transport,phytochelatin biosynthetic process, proteolysis, serine-typecarboxypeptidase activity, structural constituent of nuclear pore 46253AXg2904.t1 4433 3BXg6481.t1 E3.2.1.58. Starch and carbohydratemetabolic 0 0.021 −4.5 2.70E−02 sucrose, metabolism process, hydrolaseactivity, hydrolyzing O-glycosyl compounds, membrane part 46263AXg10815.t1 4434 3BXg9780.t1 None heme binding, oxidation- 0.125 0 72.90E−02 reduction process, peroxidase activity, response to oxidativestress 4627 3AXg2002.t1 4435 3BXg2128.t1 CNBP nucleic acid binding, zinc0.026 0 4.8 3.10E−02 ion binding 4628 3AXg3713.t1 4436 3BXg4131.t1 Nonehydrolase activity, 0.026 0 4.7 3.10E−02 metabolic process 46293AXg3872.t1 4437 3BXg4226.t1 COPB1, SEC26 COPI vesicle coat, cytosol,0.022 0 4.5 3.10E−02 ER to Golgi transport vesicle, ER to Golgivesicle-mediated transport, intracellular protein transport, kinaseactivity, phosphorylation, structural molecule activity 4630 3AXg6318.t14438 3BXg3226.t1 None hydrolase activity, 0.012 0 3.7 3.10E−02 hydrolaseactivity, acting on glycosyl bonds, organic substance metabolic process,oxidoreductase activity, primary metabolic process, single-organismmetabolic process 4631 3AXg10010.t1 4439 3BXg11186.t1 Nonedephosphorylation, 0 0.088 −6.5 3.10E−02 phosphatase activity 46323AXg1263.t1 4440 3BXg1724.t1 None chitin binding, copper ion 0.03 0 4.93.20E−02 binding, oxidation- reduction process, oxidoreductase activity4633 3AXg8122.t1 4441 3BXg9830.t1 None None 0.024 0 4.6 3.20E−02 45153AXg10862.t1 4442 3BXg9632.t1 E3.2.1.67, Pentose carbohydrate metabolic0.552 0.095 2.5 3.20E−02 and glucuronate process, cell wallinterconversions, organization, extracellular Starch and sucrose region,polygalacturonase metabolism activity 4634 3AXg5813.t1 4443 3BXg1361.t1Ascorbate and hydrolase activity, 0 0.12 −6.9 3.40E−02 aldaratemetabolism, metabolic process Caprolactam degradation, Carbonmetabolism, Degradation of aromatic compounds, E3.1.1.17, gnl, RGN,Pentose phosphate pathway 4635 3AXg2285.t1 4444 3BXg5413.t1 None hemebinding, integral 0.045 0 5.5 3.60E−02 component of membrane,oxidation-reduction process, peroxidase activity, response to oxidativestress 4636 3AXg3048.t1 4445 3BXg8570.t1 None copper ion binding, 0 0.01−3.5 3.60E−02 endoplasmic reticulum, ferrous iron import into cell,metal ion binding, oxidation-reduction process, oxidoreductase activity4637 3AXg3573.t1 4446 3BXg5567.t1 None None 0 0.019 −4.4 3.60E−02 46383AXg457.t1 4447 3BXg2952.t1 gcvH, GCSH, glycine cleavage complex, 0.0390 5.3 3.90E−02 Glycine, serine and glycine decarboxylation threoninemetabolism, via glycine cleavage Glyoxylate and system, mitochondrion,dicarboxylate one-carbon metabolic metabolism process, oxidation-reduction process, protein lipoylation 4639 3AXg2903.t1 4448 3BXg6482.t1None None 0 0.017 −4.1 3.90E−02 4640 3AXg10837.t1 4449 3BXg9608.t1 Nonecellular process, 0 0.043 −5.5 3.90E−02 membrane part, pectin catabolicprocess, pectin lyase activity 4641 3AXg10151.t1 4450 3BXg10552.t1 None1,3-beta- 0.058 0 5.9 4.10E−02 glucanosyltransfcrase activity, anchoredcomponent of membrane, ascospore wall assembly, carbohydrate metabolicprocess, endoplasmic reticulum, hydrolase activity, integral componentof membrane, plasma membrane 4642 3AXg9889.t1 4451 3BXg7932.t1 Noneextracellular region, 0.009 0 3.4 4.10E−02 mannan catabolic process,mannan endo-1,4-beta- mannosidase activity 4643 3AXg6766.t1 44523BXg3304.t1 None integral component of 0.061 0 6 4.20E−02 membrane,transmembrane transport 4644 3AXg9025.t1 4453 3BXg3854.t1 Nonecarbon-nitrogen ligase 0.015 0 4 4.20E−02 activity, with glutamine asamido-N-donor, metabolic process, transferase activity 4645 3AXg9960.t14454 3BXg7994.t1 ABC.MR ATP binding, ATPase 0 0.041 −5.4 4.20E−02activity, coupled to transmembrane movement of substances, integralcomponent of membrane, isomerase activity, metabolic process,mitochondrion, transmembrane transport 4646 3AXg8755.t1 4455 3BXg86.t1None acid phosphatase activity, 0.011 0 3.6 4.30E−02 dephosphorylation,heme binding, integral component of membrane, iron ion binding,membrane, oxidation- reduction process, oxidoreductase activity, actingon paired donors, with incorporation or reduction of molecular oxygen4647 3AXg1998.t1 4456 3BXg2125.t1 None aminopeptidase activity, 0 0.019−4.3 4.30E−02 integral component of membrane, metallopeptidase activity,proteolysis, zinc ion binding 4648 3AXg4651.t1 4457 3BXg12484.t1Nicotinate and hydrolase activity, integral 0.031 0 5 4.40E−02nicotinamide component of membrane, metabolism, Purine metabolicprocess, metabolism, substrate-specific Pyrimidine transmembranetransporter metabolism, surE activity, transmembrane transport 46493AXg1281.t1 4458 3BXg5746.t1 Antigen processing ATP binding 0.027 0 4.84.50E−02 and presentation. Endocytosis, Epstein- Barr virus infection,Estrogen signaling pathway, HSPA_18, Influenza A, Legionellosis, MAPKsignaling pathway, Measles, Protein processing in endoplasmic reticulum,Spliceosome, Toxoplasmosis 4650 3AXg2954.t1 4459 3BXg10202.t1 Nonecutinase activity, 0.02 0 4.4 4.50E−02 extracellular region, metabolicprocess 4651 3AX§8116.t1 4460 3BXg9765.t1 E3.2.1.8, xynAendo-1,4-beta-xylanase 0 0.047 −5.6 4.50E−02 activity, polysaccharidecatabolic process 4652 3AXg9229.t1 4461 3BXg511.t1 None cell cycle, celldivision, 0.02 0 4.4 4.60E−02 cyclin-dependent protein serine/threoninekinase regulator activity, integral component of membrane, regulation ofprotein kinase activity 4653 3AXg5237.t1 4462 3BXg5596.t1 Aminobenzoatemetabolic process, 0.067 0 6.1 4.70E−02 degradation, Folateoxidation-reduction biosynthesis, phoD, process Two-component system4654 3AXg9949.t1 4463 3BXg5805.t1 None None 0.061 0 6 5.00E−02 46553AXg11247.t1 4464 3BXg648.t1 None integral component of 0.009 0 3.35.00E−02 membrane 4656 3AXg9208.t1 4465 3BXg534.t1 None integralcomponent of 0.011 0.168 −3.8 5.00E−02 membrane, membrane 46573AXg7858.t1 4466 3BXg1035.t1 None flavin adenine 0 0.076 −6.3 5.00E−02dinucleotide binding, membrane, oxidation-reduction process,oxidoreductase activity, acting on CH—OH group of donors This tabledescribes the differential protein expression between pairs oforthologous proteins from a genus, where one member of the pair has abeneficial effect on plant growth and the other has a neutral effect.“A.mean” represents the average normalized spectral counts betweenbiological replicates of the beneficial member of the pair. “B.mean”represents the average normalized spectral counts betw een biologicalreplicates of the neutral member of the pair. “Fold change” representsthe fold change differenc between the two organisms. “FDR q-value”represents the false discovery rate corrected q-value.

A total of 697 proteins were detected across all Phoma samples with twoor more unique peptides at the false discovery rates indicated above.

SYM01004 Secreted Proteomic Analysis

TABLE 704 25 most abundant proteins secreted by SYM01004; “MedianAbundance” represents the median value across three biologicalreplicates in units of spectra per hundred spectra SEQ Median ID ProteinID Abundance GO Terms KEGG Terms 4742 5AYg748.t1 0.999348 GO:0005198:structural KEGG Orthology: K02406: fliC: flagellin; molecule activity;KEGG PATHWAY: ko02020: Two-component GO:0005576: extracellular system:Two-component signal transduction region; GO:0009420: systems enablebacteria to sense, respond, and bacterial-type flagellum adapt tochanges in their environment or in their filament; GO:0071973:intracellular state. Each two-component system bacterial-type flagellum-consists of a sensor protein-histidine kinase dependent cell motility(HK) and a response regulator (RR). In the prototypical two-componentpathway, the sensor HK phosphorylates its own conserved His residue inresponse to a signal(s) in the environment. Subsequently, the phosphorylgroup of HK is transferred onto a specific Asp residue on the RR. Theactivated RR can then effect changes in cellular physiology, often byregulating gene expression. Two-component pathways thus often enablecells to sense and respond to stimuli by inducing changes intranscription.; KEGG PATHWAY: ko02040: Flagellar assembly:; KEGGPATHWAY: ko04626: Plant-pathogen interaction: Plants lack animal-likeadaptive immunity mechanisms, and therefore have evolved a specificsystem with multiple layers against invading pathogens. The primaryresponse includes the perception of pathogens by cell-surfacepattern-recognition receptors (PRRs) and is referred to as PAMP-triggered immunity (PTI). Activation of FLS2 and EFR triggers MAPKsignaling pathway that activates defense genes for antimictobialcompounds. The increase in the cytosolic Ca2+ concentration is also aregulator for production of reactive oxygen species and localizedprogrammed cell death/hypersensitive response. The secondary response iscalled effector- triggered immunity (ETI). Pathogens can acquire theability to suppress PTI by directly injecting effector proteins into theplant cell through secretion systems. In addition, pathogens canmanipulate plant hormone signaling pathways to evade host immuneresponses using coronatine toxin. Some plants possess specificintracellular surveillance proteins (R proteins) to monitor the presenceof pathogen virulence proteins. This ETI occurs with localizedprogrammed cell death to arrest pathogen growth, resulting incultivar-specific disease resistance; KEGG PATHWAY: ko05132: Salmonellainfection: Salmonella infection usually presents as a self- limitinggastroenteritis or the more severe typhoid fever and bacteremia. Thecommon disease-causing Salmonella species in human is a single species,Salmonella enterica, which has numerous serovars; KEGG PATHWAY: ko05134:Legionellosis: Legionellosis is a potentially fatal infectious diseasecaused by the bacterium Legionella pneumophila and other legionellaspecies. Two distinct clinical and epidemiological syndromes areassociated with Legionella species: Legionnaires' disease is the moresevere form of the infection, which may involve pneumonia, and Pontiacfever is a milder respiratory illness. 4743 5AYg747.t1 0.973878GO:0005198: structural KEGG Orthology: K02406: fliC: flagellin; moleculeactivity; KEGG PATHWAY: ko02020: Two-component GO:0005576: extracellularsystem: Two-component signal transduction region; GO:0009420: systemsenable bacteria to sense, respond, and bacterial-type flagellum adapt tochanges in their environment or in their filament; GO:0071973:intracellular state. Each two-component system bacterial-type flagellum-consists of a sensor protein-histidine kinase dependent cell motility(HK) and a response regulator (RR). In the prototypical two-componentpathway, the sensor HK phosphorylates its own conserved His residue inresponse to a signal(s) in the environment. Subsequently, the phosphorylgroup of HK is transferred onto a specific Asp residue on the RR. Theactivated RR can then effect changes in cellular physiology, often byregulating gene expression. Two-component pathways thus often enablecells to sense and respond to stimuli by inducing changes intranscription.; KEGG PATHWAY: ko02040: Flagellar assembly:; KEGGPATHWAY: ko04626: Plant-pathogen interaction: Plants lack animal-likeadaptive immunity mechanisms, and therefore have evolved a specificsystem with multiple layers against invading pathogens. The primaryresponse includes the perception of pathogens by cell-surfacepattern-recognition receptors (PRRs) and is referred to as PAMP-triggered immunity (PTI). Activation of FLS2 and EFR triggers MAPKsignaling pathway that activates defense genes for antimictobialcompounds. The increase in the cytosolic Ca2+ concentration is also aregulator for production of reactive oxygen species and localizedprogrammed cell death/hypersensitive response. The secondary response iscalled effector-triggered immunity (ETI). Pathogens can acquire theability to suppress PTI by directly injecting effector proteins into theplant cell through secretion systems. In addition, pathogens canmanipulate plant hormone signaling pathways to evade host immuneresponses using coronatine toxin. Some plants possess specificintracellular surveillance proteins (R proteins) to monitor the presenceof pathogen virulence proteins. This ETI occurs with localizedprogrammed cell death to arrest pathogen growth, resulting incultivar-specific disease resistance.; KEGG PATHWAY: ko05132: Salmonellainfection: Salmonella infection usually presents as a self-limitinggastroenteritis or the more severe typhoid fever and bacteremia. Thecommon disease- causing Salmonella species in human is a single species,Salmonella enterica, which has numerous serovars.; KEGG PATHWAY:ko05134: Legionellosis: Legionellosis is a potentially fatal infectiousdisease caused by the bacterium Legionella pneumophila and otherlegionella species. Two distinct clinical and epidemiological syndromesare associated with Legionella species: Legionnaires' disease is themore severe form of the infection, which may involve pneumonia, andPontiac fever is a milder respiratory illness. 4744 5AYg746.t1 0.393566GO:0005198: structural KEGG Orthology: K02406: fliC: flagellin; moleculeactivity; KEGG PATHWAY: ko02020: Two-component GO:0005576: extracellularsystem: Two-component signal transduction region; GO:0009420: systemsenable bacteria to sense, respond, and bacterial-type flagellum adapt tochanges in their environment or in their filament; GO:0071973:intracellular state. Each two-component system bacterial-type flagellum-consists of a sensor protein-histidine kinase dependent cell motility(HK) and a response regulator (RR). In the prototypical two-componentpathway, the sensor HK phosphorylates its own conserved His residue inresponse to a signal(s) in the environment. Subsequently, the phosphorylgroup of HK is transferred onto a specific Asp residue on the RR. Theactivated RR can then effect changes in cellular physiology, often byregulating gene expression. Two-component pathways thus often enablecells to sense and respond to stimuli by inducing changes intranscription.; KEGG PATHWAY: ko02040: Flagellar assembly:; KEGGPATHWAY: ko04626: Plant-pathogen interaction: Plants lack animal-likeadaptive immunity mechanisms, and therefore have evolved a specificsystem with multiple layers against invading pathogens. The primaryresponse includes the perception of pathogens by cell-surfacepattern-recognition receptors (PRRs) and is referred to as PAMP-triggered immunity (PTI). Activation of FLS2 and EFR triggers MAPKsignaling pathway that activates defense genes for antimictobialcompounds. The increase in the cytosolic Ca2+ concentration is also aregulator for production of reactive oxygen species and localizedprogrammed cell death/hypersensitive response. The secondary response iscalled effector- triggered immunity (ETI). Pathogens can acquire theability to suppress PTI by directly injecting effector proteins into theplant cell through secretion systems. In addition, pathogens canmanipulate plant hormone signaling pathways to evade host immuneresponses using coronatine toxin. Some plants possess specificintracellular surveillance proteins (R proteins) to monitor the presenceof pathogen virulence proteins. This ETI occurs with localizedprogrammed cell death to arrest pathogen growth, resulting incultivar-specific disease resistance.; KEGG PATHWAY: ko05132: Salmonellainfection: Salmonella infection usually presents as a self-limitinggastroenteritis or the more severe typhoid fever and bacteremia. Thecommon disease- causing Salmonella species in human is a single species,Salmonella enterica, which has numerous serovars.; KEGG PATHWAY:ko05134: Legionellosis: Legionellosis is a potentially fatal infectiousdisease caused by the bacterium Legionella pneumophila and otherlegionella species. Two distinct clinical and epidemiological syndromesare associated with Legionella species: Legionnaires' disease is themore severe form of the infection, which may involve pneumonia, andPontiac fever is a milder respiratory illness. 4745 5AYg329.t1 0.208236GO:0004519: endonuclease KEGG Orthology: K00940: ndk, NME: activity;GO:0004550: nucleoside-diphosphate kinase [EC:2.7.4.6]; nucleosidediphosphate KEGG PATHWAY: ko00230: Purine kinase activity; metabolism:;KEGG PATHWAY: ko00240: GO:0005524: ATP binding; Pyrimidine metabolism:GO:0005737: cytoplasm; GO:0006165: nucleoside diphosphatephosphorylation; GO:0006183: GTP biosynthetic process; GO:0006228: UTPbiosynthetic process; GO:0006241: CTP biosynthetic process; GO:0046872:metal ion binding; GO:0090305: nucleic acid phosphodiester bondhydrolysis 4746 5AYg1483.t1 0.204231 GO:0015288: porin activity; noneGO:0016020: membrane; GO:0055085: transmembrane transport 47475AYg1901.t1 0.201732 GO:0004970: ionotropic KEGG Orthology: K02030:ABC.PA.S: polar glutamate receptor activity; amino acid transport systemsubstrate-binding GO:0006810: transport; protein GO:0016020: membrane;GO:0030288: outer membrane-bounded periplasmic space; GO:0035235:ionotropic glutamate receptor signaling pathway 4748 5AYg2621.t10.184662 GO:0003735: structural KEGG Orthology: K02884: RP-L19, MRPL19,constituent of ribosome; rplS: large subunit ribosomal protein L19;GO:0005840: ribosome; KEGG PATHWAY: ko03010: Ribosome: GO:0006412:translation 4749 5AYg1882.t1 0.177 GO:0003735: structural KEGGOrthology: K02879: RP-L17, MRPL17, constituent of ribosome; rplQ: largesubunit ribosomal protein L17; GO:0005840: ribosome; KEGG PATHWAY:ko03010: Ribosome: GO:0006412: translation 4750 5AYg89.t1 0.175201GO:0000049: tRNA KEGG Orthology: K02992: RP-S7, MRPS7, binding;GO:0003735: rpsG: small subunit ribosomal protein S7; structuralconstituent of KEGG PATHWAY: ko03010: Ribosome: ribosome; GO:0006412:translation; GO:0015935: small ribosomal subunit; GO:0019843: rRNAbinding 4751 5AYg1281.t1 0.167696 GO:0006935: chemotaxis; KEGGOrthology: K10546: ABC.GGU.S, chvE: GO:0042597: periplasmic putativemultiple sugar transport system space substrate-binding protein; KEGGPATHWAY: ko02010: ABC transporters: The ATP-binding cassette (ABC)transporters form one of the largest known protein families, and arewidespread in bacteria, archaea, and eukaryotes. They couple ATPhydrolysis to active transport of a wide variety of substrates such asions, sugars, lipids, sterols, peptides, proteins, and drugs. Thestructure of a prokaryotic ABC transporter usually consists of threecomponents; typically two integral membrane proteins each having sixtransmembrane segments, two peripheral proteins that bind and hydrolyzeATP, and a periplasmic (or lipoprotein) substrate- binding protein. Manyof the genes for the three components form operons as in fact observedin many bacterial and archaeal genomes. On the other hand, in a typicaleukaryotic ABC transporter, the membrane spanning protein and theATP-binding protein are fused, forming a multi-domain protein with themembrane- spanning domain (MSD) and the nucleotide- binding domain(NBD). 4752 5AYg777.t1 0.156177 GO:0000413: protein KEGG Orthology:K03768: PPIB, ppiB: peptidyl-prolyl peptidyl-prolyl cis-trans isomeraseB isomerization; (cyclophilin B) [EC:5.2.1.8] GO:0003755: peptidyl-prolyl cis-trans isomerase activity; GO:0006457: protein folding 47535AYg1692.t1 0.155178 GO:0003677: DNA KEGG Orthology: K03704: cspA: coldshock binding; GO:0005737: protein (beta-ribbon, CspA family) cytoplasm;GO:0006355: regulation of transcription, DNA-templated 4754 5AYg1247.t10.152662 GO:0006865: amino acid KEGG Orthology: K01999: livK: branched-transport chain amino acid transport system substrate- binding protein;KEGG PATHWAY: ko02010: ABC transporters: The ATP-binding cassette (ABC)transporters form one of the largest known protein families, and arewidespread in bacteria, archaea, and eukaryotes. They couple ATPhydrolysis to active transport of a wide variety of substrates such asions, sugars, lipids, sterols, peptides, proteins, and drugs. Thestructure of a prokaryotic ABC transporter usually consists of threecomponents; typically two integral membrane proteins each having sixtransmembrane segments, two peripheral proteins that bind and hydrolyzeATP, and a periplasmic (or lipoprotein) substrate-binding protein. Manyof the genes for the three components form operons as in fact observedin many bacterial and archaeal genomes. On the other hand, in a typicaleukaryotic ABC transporter, the membrane spanning protein and theATP-binding protein are fused, forming a multi-domain protein with themembrane- spanning domain (MSD) and the nucleotide- binding domain(NBD). 4755 5AYg2256.t1 0.149078 GO:0016021: integral KEGG Orthology:K16079: omp31: outer component of membrane membrane immunogenic protein4756 5AYg208.t1 0.14751 GO:0003735: structural KEGG Orthology: K02986:RP-S4, rpsD: small constituent of ribosome; subunit ribosomal proteinS4; KEGG GO:0006412: translation; PATHWAY: ko03010: Ribosome:GO:0015935: small ribosomal subunit; GO:0019843: rRNA binding 47575AYg1876.t1 0.146416 GO:0000049: tRNA KEGG Orthology: K02931: RP-L5,MRPL5, binding; GO:0003735: rplE: large subunit ribosomal protein L5;KEGG structural constituent of PATHWAY: ko03010: Ribosome: ribosome;GO:0005840: ribosome; GO:0006412: translation; GO:0019843: rRNA binding4758 5AYg998.t1 0.145775 GO:0004801: KEGG Orthology: K00616: E2.2.1.2,talA, talB: sedoheptulose-7- transaldolase [EC:2.2.1.2]; KEGG PATHWAY:phosphate:D- ko00030: Pentose phosphate pathway: Theglyceraldehyde-3-phosphate pentose phosphate pathway is a process ofglyceronetransferase glucose turnover that produces NADPH as activity;GO:0005737: reducing equivalents and pentoses as essential cytoplasm;GO:0005975: parts of nucleotides. There are two different carbohydratemetabolic phases in the pathway. One is irreversible process;GO:0006098: oxidative phase in which glucose-6P is pentose-phosphateshunt converted to ribulose-5P by oxidative decarboxylation, and NADPHis generated [MD:M00006]. The other is reversible non- oxidative phasein which phosphorylated sugars are interconverted to generatexylulose-5P, ribulose-5P, and ribose-5P [MD:M00007]. Phosphoribosylpyrophosphate (PRPP) formed from ribose-5P [MD:M00005] is an activatedcompound used in the biosynthesis of histidine and purine/pyrimidinenucleotides. This pathway map also shows the Entner-Doudoroff pathwaywhere 6-P-gluconate is dehydrated and then cleaved into pyruvate andglyceraldehyde-3P [MD:M00008].; KEGG PATHWAY: ko01200: Carbonmetabolism: Carbon metabolism is the most basic aspect of life. This mappresents an overall view of central carbon metabolism, where the numberof carbons is shown for each compound denoted by a circle, excluding acofactor (CoA, CoM, THF, or THMPT) that is replaced by an asterisk. Themap contains carbon utilization pathways of glycolysis (map00010),pentose phosphate pathway (map00030), and citrate cycle (map00020), andsix known carbon fixation pathways (map00710 and map00720) as well assome pathways of methane metabolism (map00680). The six carbon fixationpathways are: (1) reductive pentose phosphate cycle (Calvin cycle) inplants and cyanobacteria that perform oxygenic photosynthesis, (2)reductive citrate cycle in photosynthetic green sulfur bacteria and somechemolithoautotrophs, (3) 3-hydroxypropionate bi-cycle in photosyntheticgreen nonsulfur bacteria, two variants of 4-hydroxybutyrate pathways inCrenarchaeota called (4) hydroxypropionate-hydroxybutyrate cycle and (5)dicarboxylate-hydroxybutyrate cycle, and (6) reductive acetyl-CoApathway in methanogenic bacteria.; KEGG PATHWAY: ko01230: Biosynthesisof amino acids: This map presents a modular architecture of thebiosynthesis pathways of twenty amino acids, which may be viewed asconsisting of the core part and its extensions. The core part is theKEGG module for conversion of three-carbon compounds fromglyceraldehyde-3P to pyruvate [MD:M00002], together with the pathwaysaround serine and glycine. This KEGG module is the most conserved one inthe KEGG MODULE database and is found in almost all the completelysequenced genomes. The extensions are the pathways containing thereaction modules RM001, RM033, RM032, and RM002 for biosynthesis ofbranched-chain amino acids (left) and basic amino acids (bottom), andthe pathways for biosynthesis of histidine and aromatic amino acids (topright). It is interesting to note that the so-called essential aminoacids that cannot be synthesized in human and other organisms generallyappear in these extensions. Furthermore, the bottom extension of basicamino acids appears to be most divergent containing multiple pathwaysfor lysine biosynthesis and multiple gene sets for argininebiosynthesis. 4759 5AYg1162.t1 0.144833 GO:0006006: glucose KEGGOrthology: K00134: GAPDH, gapA: metabolic process; glyceraldehyde3-phosphate dehydrogenase GO:0016620: [EC: 1.2.1.12]; KEGG PATHWAY:ko00010: oxidoreductase activity, Glycolysis/Gluconeogenesis: Glycolysisis the acting on the aldehyde or process of converting glucose intopyruvate and oxo group of donors, NAD generating small amounts of ATP(energy) and or NADP as acceptor; NADH (reducing power). It is a centralpathway GO:0050661: NADP that produces important precursor metabolites:binding; GO:0051287: six-carbon compounds of glucose-6P and NAD binding;fructose-6P and three-carbon compounds of GO:0055114: oxidation-glycerone-P, glyceraldehyde-3P, glycerate-3P, reduction processphosphoenolpyruvate, and pyruvate [MD:M00001]. Acetyl-CoA, anotherimportant precursor metabolite, is produced by oxidative decarboxylationof pyruvate [MD:M00307], When the enzyme genes of this pathway areexamined in completely sequenced genomes, the reaction steps ofthree-carbon compounds from glycerone-P to pyruvate form a conservedcore module [MD:M00002], which is found in almost all organisms andwhich sometimes contains operon structures in bacterial genomes.Gluconeogenesis is a synthesis pathway of glucose from noncarbohydrateprecursors. It is essentially a reversal of glycolysis with minorvariations of alternative paths [MD:M00003].; KEGG PATHWAY: ko00710:Carbon fixation in photosynthetic organisms:; KEGG PATHWAY: ko01200:Carbon metabolism: Carbon metabolism is the most basic aspect of life.This map presents an overall view of central carbon metabolism, wherethe number of carbons is shown for each compound denoted by a circle,excluding a cofactor (CoA, CoM, THF, or THMPT) that is replaced by anasterisk. The map contains carbon utilization pathways of glycolysis(map00010), pentose phosphate pathway (map00030), and citrate cycle(map00020), and six known carbon fixation pathways (map00710 andmap00720) as well as some pathways of methane metabolism (map00680). Thesix carbon fixation pathways are: (1) reductive pentose phosphate cycle(Calvin cycle) in plants and cyanobacteria that perform oxygenicphotosynthesis, (2) reductive citrate cycle in photosynthetic greensulfur bacteria and some chemolithoautotrophs, (3) 3- hydroxypropionatebi-cycle in photosynthetic green nonsulfur bacteria, two variants of 4-hydroxybutyrate pathways in Crenarchaeota called (4)hydroxypropionate-hydroxybutyrate cycle and (5)dicarboxylate-hydroxybutyrate cycle, and (6) reductive acetyl-CoApathway in methanogenic bacteria.; KEGG PATHWAY: ko01230: Biosynthesisof amino acids: This map presents a modular architecture of thebiosynthesis pathways of twenty amino acids, which may be viewed asconsisting of the core part and its extensions. The core part is theKEGG module for conversion of three-carbon compounds fromglyceraldehyde-3P to pyruvate [MD:M00002], together with the pathwaysaround serine and glycine. This KEGG module is the most conserved one inthe KEGG MODULE database and is found in almost all the completelysequenced genomes. The extensions are the pathways containing thereaction modules RM001, RM033, RM032, and RM002 for biosynthesis ofbranched-chain amino acids (left) and basic amino acids (bottom), andthe pathways for biosynthesis of histidine and aromatic amino acids (topright). It is interesting to note that the so-called essential aminoacids that cannot be synthesized in human and other organisms generallyappear in these extensions. Furthermore, the bottom extension of basicamino acids appears to be most divergent containing multiple pathwaysfor lysine biosynthesis and multiple gene sets for argininebiosynthesis.; KEGG PATHWAY: ko04066: HIF-1 signaling pathway: Hypoxia-inducible factor 1 (HIF-1) is a transcription factor that functions as amaster regulator of oxygen homeostasis. It consists of two subunits: aninducibly-expressed HIF-1alpha subunit and a constitutively-expressedHIF-1beta subunit. Under normoxia, HIF-1 alpha undergoes hydroxylationat specific prolyl residues which leads to an immediate ubiquitinationand subsequent proteasomal degradation of the subunit. In contrast,under hypoxia, HIF-1 alpha subunit becomes stable and interacts withcoactivators such as p300/CBP to modulate its transcriptional activity.Eventually, HIF-1 acts as a master regulator of numerous hypoxia-inducible genes under hypoxic conditions. The target genes of HIF-1encode proteins that increase O2 delivery and mediate adaptive responsesto O2 deprivation. Despite its name, HIF-1 is induced not only inresponse to reduced oxygen availability but also by other stimulants,such as nitric oxide, or various growth factors.; KEGG PATHWAY: ko05010:Alzheimer's disease: Alzheimer's disease (AD) is a chronic disorder thatslowly destroys neurons and causes serious cognitive disability. AD isassociated with senile plaques and neurofibrillary tangles (NFTs).Amyloid-beta (Abeta), a major component of senile plaques, has variouspathological effects on cell and organelle function. The extracellularAbeta oligomers may activate caspases through activation of cell surfacedeath receptors. Alternatively, intracellular Abeta may contribute topathology by facilitating tau hyper-phosphorylation, disruptingmitochondria function, and triggering calcium dysfunction. To dategenetic studies have revealed four genes that may be linked to autosomaldominant or familial early onset AD (FAD). These four genes include:amyloid precursor protein (APP), presenilin 1 (PS1), presenilin 2 (PS2)and apolipoprotein E (ApoE). All mutations associated with APP and PSproteins can lead to an increase in the production of Abeta peptides,specfically the more amyloidogenic form, Abeta42. FAD-linked PS1mutation downregulates the unfolded protein response and leads tovulnerability to ER stress. 4760 5AYg287.t1 0.138824 GO:0003677: DNAKEGG Orthology: K03530: hupB: DNA-binding binding; GO:0030261: proteinHU-beta chromosome condensation 4761 5AYg677.t1 0.137328 GO:0005524: ATPbinding; KEGG Orthology: K04077: groEL, HSPD1: GO:0005737: cytoplasm;chaperonin GroEL; KEGG PATHWAY: GO:0016491: ko03018: RNA degradation:The correct oxidoreductase activity; processing, quality control andturnover of GO:0042026: protein cellular RNA molecules are critical tomany refolding; GO:0051082: aspects in the expression of geneticinformation. unfolded protein binding; In eukaryotes, two major pathwaysof mRNA GO:0055114: oxidation- decay exist and both pathways areinitiated by reduction process poly(A) shortening of the mRNA. In the 5′to 3′ pathway, this is followed by decapping which then permits the 5′to 3′ exonucleolytic degradation of transcripts. In the 3′ to 5′pathway, the exosome, a large multisubunit complex, plays a key role.The exosome exists in archaeal cells, too. In bacteria, endoribonucleaseE, a key enzyme involved in RNA decay and processing, organizes aprotein complex called degradosome. RNase E or R interacts with thephosphate-dependent exoribonuclease polynucleotide phosphorylase,DEAD-box helicases, and additional factors in the RNA- degradingcomplex.; KEGG PATHWAY: ko04940: Type I diabetes mellitus: Type Idiabetes mellitus is a disease that results from autoimmune destructionof the insulin-producing beta-cells. Certain beta-cell proteins act asautoantigens after being processed by antigen- presenting cell (APC),such as macrophages and dendritic cells, and presented in a complex withMHC-II molecules on the surface of the APC. Then immunogenic signalsfrom APC activate CD4+ T cells, predominantly of the Th1 subset.Antigen-activated Th1 cells produce IL-2 and IFNgamma. They activatemacrophages and cytotoxic CD8+ T cells, and these effector cells maykill islet beta-cells by one or both of two types of mechanisms: (1)direct interactions of antigen-specific cytotoxic T cells with a beta-cell autoantigen-MHC-I complex on the beta- cell, and (2) non-specificinflammatory mediators, such as free radicals/oxidants and cytokines(IL-1, TNFalpha, TNFbeta, IFNgamma).; KEGG PATHWAY: ko05134:Legionellosis: Legionellosis is a potentially fatal infectious diseasecaused by the bacterium Legionella pneumophila and other legionellaspecies. Two distinct clinical and epidemiological syndromes areassociated with Legionella species: Legionnaires' disease is the moresevere form of the infection, which may involve pneumonia, and Pontiacfever is a milder respiratory illness.; KEGG PATHWAY: ko05152:Tuberculosis: Tuberculosis, or TB, is an infectious disease caused byMycobacterium tuberculosis. One third of the world's population isthought to be infected with TB. About 90% of those infected result inlatent infections, and about 10% of latent infections develop activediseases when their immune system is impaired due to the age, otherdiseases such as AIDS or exposure to immunosuppressive drugs. TB istransmitted through the air and primarily attacks the lungs, then it canspread by the circulatory system to other parts of body. Once TB bacillihave entered the host by the respiratory route and infected macrophagesin the lungs, they interfere with phagosomal maturation, antigenpresentation, apoptosis and host immune system to establish persistentor latent infection. 4762 5AYg2260.t1 0.135 GO:0043190: ATP-binding KEGGOrthology: K12368: dppA: dipeptide cassette (ABC) transporter transportsystem substrate-binding protein; complex; GO:0055085: KEGG PATHWAY:ko02010: ABC transmembrane transport transporters: The ATP-bindingcassette (ABC) transporters form one of the largest known proteinfamilies, and are widespread in bacteria, archaea, and eukaryotes. Theycouple ATP hydrolysis to active transport of a wide variety ofsubstrates such as ions, sugars, lipids, sterols, peptides, proteins,and drugs. The structure of a prokaryotic ABC transporter usuallyconsists of three components; typically two integral membrane proteinseach having six transmembrane segments, two peripheral proteins thatbind and hydrolyze ATP, and a periplasmic (or lipoprotein)substrate-binding protein. Many of the genes for the three componentsform operons as in fact observed in many bacterial and archaeal genomes.On the other hand, in a typical eukaryotic ABC transporter, the membranespanning protein and the ATP-binding protein are fused, forming amulti-domain protein with the membrane- spanning domain (MSD) and thenucleotide- binding domain (NBD).; KEGG PATHWAY: ko02030: Bacterialchemotaxis: Chemotaxis is the process by which cells sense chemicalgradients in their environment and then move towards more favorableconditions. In chemotaxis, events at the receptors controlautophosphorylation of the CheA histidine kinase, and thephosphohistidine is the substrate for the response regulator CheY, whichcatalyzes the transfer of the phosphoryl group to a conserved aspartate.The resulting CheY-P can interact with the switch mechanism in themotor. This interaction causes a change in behavior, such as indirection or speed of rotation of flagella. 4763 5AYg980.t1 0.133866GO:0016021: integral KEGG Orthology: K16079: omp31: outer component ofmembrane membrane immunogenic protein 4764 5AYg2744.t1 0.131774GO:0000413: protein KEGG Orthology: K03769: ppiC: peptidyl-peptidyl-prolyl prolyl cis-trans isomerase C [EC:5.2.1.8] isomerization;GO:0003755: peptidyl- prolyl cis-trans isomerase activity 47655AYg2575.t1 0.130147 GO:0003735: structural KEGG Orthology: K02899:RP-L27, MRPL27, constituent of ribosome; rpmA: large subunit ribosomalprotein L27; GO:0005840: ribosome; KEGG PATHWAY: ko03010: Ribosome:GO:0006412: translation; GO:0019843: rRNA binding 4766 5AYg676.t10.128736 GO:0005524: ATP binding; KEGG Orthology: K04078: groES, HSPE1:G0:0005737: cytoplasm; chaperonin GroES GO:0006457: protein folding

SYM01004 Versus SYM00091

TABLE 705 Differential secreted protein abundance between SYM01004 andSYM00091. SEQ ID SEQ ID Fold- FDR Beneficial A.protein Neutral B.proteinKEGG GO A.mean B.mean change q-value 4734 5AYg1329.t1 4671 5BYg3790.t1ade, Purine adenine catabolic 0.057 0  5.9 3.90E−02 metabolism process,adenine deaminase activity 4735 5AYg1185.t1 4672 5BYg649.t1 Biosynthesisof L-serine 0 0.009 −3.3 4.90E−02 amino acids, Carbon biosyntheticmetabolism, Glycine, process, NAD serine and threonine binding,oxidation- metabolism, Methane reduction process, metabolism, serA,phosphoglycerate PHGDH dehydrogenase activity 4736 5AYg1107.t1 46735BYg1291.t1 ABC transporters, ATP binding, ATP- 0.008 0  3.2 4.40E−02ABC.MS.S, msmX, binding cassette msmK, malK, sugC, (ABC) transporterggtA, msiK complex, ATPase activity, carbohydrate transport, hydrolaseactivity, acting on acid anhydrides, catalyzing transmembrane movementof substances, metabolic process, transmembrane transport, transporteractivity 4737 5AYg1262.t1 4674 5BYg1034.t1 None integral component 00.007 −3.1 4.00E−02 of membrane, transport, transporter activity 47385AYg1075.t1 4675 5BYg577.t1 E2.4.1.1, glgP, PYG, carbohydrate 0 0.007−2.9 3.00E−02 Insulin signaling metabolic process, pathway, Starch andglycogen sucrose metabolism phosphorylase activity, pyridoxal phosphatebinding 4739 5AYg1184.t1 4676 5BYg648.t1 Biosynthesis of aminocytoplasm, L-serine 0.036 0.005  2.7 4.90E−02 acids, Carbon biosyntheticmetabolism, Glycine, process, serine and threonine O-phospho-L-metabolism, Methane serine: 2- metabolism, serC, oxoglutarate PSAT1,Vitamin B6 aminotransferase metabolism activity 4740 5AYg126.t1 46775BYg3243.t1 Carbon metabolism, glycine 0.032 0.006  2.2 3.90E−02 GLDC,gcvP, Glycine, decarboxylation serine and threonine via glycinemetabolism cleavage system, glycine dehydrogenase (decarboxylating)activity, lyase activity, oxidation- reduction process 4741 5AYg124.t14678 5BYg3241.t1 K09796 None 0.019 0.004  2.1 3.90E−02 This tabledescribes the differential protein expression between pairs oforthologous proteins from a genus, where one member of the pair has abeneficial effect on plant growth and the other has a neutral effect.“A.mean” represents the average normalized spectral counts betweenbiological replicates of the beneficial member of the pair. “B.mean”represents the average normalized spectral counts between biologicalreplicates of the neutral member of the pair. “Fold change” representsthe fold change differenc between the two organisms. “FDR q-value”represents the false discovery rate corrected q-value.

A total of 1390 proteins were detected across all Agrobacterium sampleswith two or more unique peptides at the false discovery rates indicatedabove.

KEGG Pathway Enrichment of Beneficial Fungi Versus Neutral Fungi

TABLE 706 KEGG Pathway enrichment of beneficial fungi versus neutralfungi KEGG SEQ ID SEQ ID FDR Category ID Name Description BeneficialA.Protein.ID Neutral B.Protein.ID q-value KEGG ko00500 Starch and none643; 2293; 1AXg13171.t1, 4104; 1BXg10106.t1, 2.92E−10 PATHWAY sucrose2292; 874; 1AXg2246.t1, 4126; 1BXg10460.t1, metabolism 480; 2288;1AXg2742.t1, 4125; 1BXg10656.t1, 487; 2285; 1AXg2815.t1, 2443;1BXg1289.t1, 580; 2279; 1AXg3149.t1, 4097; 1BXg135.t1, 4543;1AXg4053.t1, 4122; 1BXg1561.t1, 4515; 1AXg5358.t1, 2349; 1BXg2692.t1,4669; 1AXg5538.t1, 4118; 1BXg3232.t1, 4668; 1AXg5751.t1, 2382;1BXg3531.t1, 4666; 1AXg8814.t1, 2436; 1BXg4362.t1, 4615; 3AXg10791.t1,2377; 1BXg4998.t1, 4573; 3AXg10862.t1, 2350; 1BXg5592.t1, 4661;3AXg1436.t1, 2721; 1BXg9114.t1, 4659; 3AXg192.t1, 2470; 1BXg9824.t1,4571 3AXg2790.t1, 4508; 3BXg11320.t1, 3AXg4536.t1, 4413; 3BXg14385.t1,3AXg4810.t1, 4507; 3BXg1864.t1, 3AXg6314.t1, 4505; 3BXg2317.t1,3AXg7872.t1, 4422; 3BXg3121.t1, 3AXg9121.t1 4500; 3BXg3387.t1, 4433;3BXg6481.t1, 4410; 3BXg6843.t1, 4423; 3BXg6890.t1, 4491; 3BXg7356.t1,4487; 3BXg928.t1, 4442; 3BXg9632.t1, 4346; 3BXg9786.t1, 4484 3BXg9960.t1KEGG K08257 E3.2.1.101 mannan endo- 2277; 528; 1AXg10033.t1, 2457;1BXg12075.t1, 2.62E−05 Orthology 1,6-alpha- 623; 2278; 1AXg4291.t1,4121; 1BXg1595.t1, mannosidase 4663; 1AXg459.t1, 4112; 1BXg6031.t1, [EC:3.2.1.101] 4585 1AXg9931.t1, 2422; 1BXg8019.t1, 3AXg512.t1, 4391;3BXg10636.t1, 3AXg7050.t1 4499; 3BXg3817.t1, 4492 3BXg7176.t1 KEGGK18576 XEG xyloglucan- 2273; 1AXg6048.t1, 2390; 1BXg307.t1, 4.04E−05Orthology specific endo- 1249; 1AXg9842.t1, 4109; 1BXg8240.t1, beta-1,4-4540 3AXg10237.t1 3093; 1BXg9770.t1, glucanase 4509; 3BXg10794.t1, [EC:3.2.1.151] 4343 3BXg1101.t1 KEGG ko00040 Pentose and none 480; 4515;1AXg3149.t1, 4099; 1BXg12260.t1, 0.000335 PATHWAY glucuronate 4666;3AXg10862.t1, 2377; 1BXg4998.t1, interconversion 4571 3AXg2790.t1, 4106;1BXg941.t1, 3AXg9121.t1 4442 3BXg9632.t1 KEGG K00505 TYR tyrosinase2275; 1AXg11951.t1, 4096; 1BXg5424.t1, 0.002931 Orthology [EC:1.14.18.1] 4609; 3AXg2591.t1, 4113; 1BXg5696.t1, 4528; 3AXg2961.t1,4415; 3BXg1833.t1, 4660 3AXg6319.t1 4501; 3BXg3225.t1, 4369; 3BXg390.t1,4498; 3BXg3977.t1, 4495; 3BXg6039.t1, 4394; 3BXg8171.t1, 44883BXg8955.t1 KEGG ko00052 Galactose none 874; 2291; 1AXg2815.t1, 4097;1BXg135.t1, 0.003136 PATHWAY metabolism 4669; 1AXg325.t1, 2382;1BXg3531.t1, 4615; 3AXg1436.t1, 2350; 1BXg5592.t1, 4661 3AXg4536.t1,2721; 1BXg9114.t1, 3AXg6314.t1 4508; 3BXg11320.t1, 4422; 3BXg3121.t1,4496; 3BXg5975.t1, 4494; 3BXg6701.t1, 4410; 3BXg6843.t1, 4491;3BXg7356.t1, 4484 3BXg9960.t1 KEGG ko00965 Betalain Betalains are 2275;1AXg11951.t1, 4096; 1BXg5424.t1, 0.003618 PATHWAY biosynthesiswater-soluble 4609; 3AXg2591.t1, 4113; 1BXg5696.t1, nitrogen- 4528;3AXg2961.t1, 4415; 3BXg1833.t1, containing 4660 3AXg6319.t1 4501;3BXg3225.t1, pigments that 4369; 3BXg390.t1, are present in 4498;3BXg3977.t1, plants 4495; 3BXg6039.t1, belonging to 4394; 3BXg8171.t1,the order 4488 3BXg8955.t1 Caryoplyllales (such as cactus and amaranthfamilies) and in higher fungi. They contain betalamic acid as thechromophore and are classified into two types: betacyanins andbetaxanthins. Betacyanins contain a cyclo-DOPA residue and exhibitred/violet coloration, while betaxanthins contain different amino acidsor amino side chains and exhibit a yellow/orange coloration. Thecondensation of betalamic acid with amino acids (including cyclo-DOPA oramines) in plants is a spontaneous reaction, not an enzyme- catalvzedreaction.

Melanogenesis Cutaneous 2275; 665; 1AXg11951.t1, 2320; 1BXg11664.t1,0.005636 melanin 4609; 1AXg4299.t1, 4096; 1BXg5424.t1, pigment plays4528; 3AXg2591.t1, 4113; 1BXg5696.t1, a critical role 4660 3AXg2961.t1,4415; 3BXg1833.t1, in 3AXg6319.t1 4501; 3BXg3225.t1, camouflage, 4369;3BXg390.t1, mimicry, 4498; 3BXg3977.t1, social 4495; 3BXg6039.t1,communication, 4394; 3BXg8171.t1, and 4488 3BXg8955.t1 protectionagainst harmful effects of solar radiation. Melanogenesis is undercomplex regulatory control by multiple agents. The most importantpositive regulator of melanogenesis is the MC1 receptor with its ligandsmelanocortic peptides. MC1R activates the cyclic AMP (cAMP) response-element binding protein (CREB). Increased expression of MITF and itsactivation by phosphorylation (P) stimulate the transcription oftyrosinase (TYR), tyrosinase- related protein 1 (TYRP1), and dopachrometautomerase (DCT), which produce melanin. Melanin synthesis takes placewithin specialized intracellular

KEGG ko04142 Lysosome Lysosomes 521; 2295; 1AXg11059.t1, 4102;1BXg10249.t1, 0.009426 PATHWAY are 608; 2290; 1AXg12307.t1, 4124;1BXg11338.t1, membrane- 2289; 1AXg1785.t1, 2407; 1BXg1175.t1, delimited2286; 1AXg3652.t1, 4116; 1BXg4075.t1, organelles in 2282; 1AXg3653.t1,4111; 1BXg7402.t1, animal cells 4559; 1AXg5534.t1, 4107; 1BXg9090.t1,serving as the 4670; 1AXg7972.t1, 4506; 3BXg2203.t1, cell's main 4665;3AXg10485.t1, 4353; 3BXg4014.t1, digestive 4525; 3AXg10865.t1, 4497;3BXg4508.t1, compartment 4526; 3AXg3114.t1, 4432; 3BXg5175.t1, to whichall 4624 3AXg5987.t1, 4386; 3BXg5319.t1, sorts of 3AXg8810.t1, 4362;3BXg821.t1, macromolecules 3AXg9670.t1 4485 3BXg9634.t1 are deliveredfor degradation. They contain more than 40 hydrolases in an acidicenvironment (pH of about 5). After synthesis in the ER, lysosomalenzymes are decorated with mannose-6- phosphate residues, which arerecognized by mannose-6- phosphate receptors in the trans- Golginetwork. They are packaged into clathrin- coated vesicles and aretransported to late endosomes. Substances for digestion are acquired bythe lysosomes via a series of processes including endocytosis,phagocytosis, and antophagy. KEGG ko00950 Isoquinoline Isoquinoline2275; 1AXg11951.t1, 4098; 1BXg12278.t1, 0.011241 PATHWAY alkaloidalkaloids are 1342; 1AXg7766.t1, 4119; 1BXg2903.t1, biosynthesistyrosine- 4609; 3AXg2591.t1, 4096; 1BXg5424.t1, derived plant 4528;3AXg2961.t1, 4113; 1BXg5696.t1, alkaloids with 4660 3AXg6319.t1 4108;1BXg8510.t1, an 3185; 1BXg886.t1, isoquinoline 4415; 3BXg1833.t1,skeleton. 4501; 3BXg3225.t1, Among them 4369; 3BXg390.t1,benzylisoquinoline 4498; 3BXg3977.t1, alkaloids 4495; 3BXg6039.t1, forman 4493; 3BXg6827.t1, important 4394; 3BXg8171.t1, group with 4488;3BXg8955.t1 potent pharmacological activity, including analgesiccompounds of morphine and codeine, and anti-infective agents ofberberine. palmatine, and magnoflorine. Biosynthesis of isoquinolinealkaloids proceeds via decarboxylation of tyrosine or DOPA to yielddopamine, which together with 4- hydroxyphenyl- acetaldehyde, analdehyde derived from tyrosine, is converted to reticuline, an importantprecursor of various benzylisoquinoline alkaloids. KEGG ko00630Glyoxylate none 2272; 1AXg6636.t1, 4103; 1BXg10186.t1, 0.011241 PATHWAYand 4638; 3AXg457.t1, 2315; 1BXg2840.t1, dicarboxylate 4658 3AXg9876.t14110; 1BXg7797.t1, metabolism 4490 3BXg7921.t1 KEGG ko00740 Riboflavinnone 2275; 485; 1AXg11951.t1, 4100; 1BXg11698.t1, 0.011241 PATHWAYmetabolism 496; 663; 1AXg1240.t1, 4123; 1BXg11921.t1, 2283;1AXg13882.t1, 4117; 1BXg3956.t1, 2280; 1AXg4563.t1, 2464; 1BXg4094.t1,4609; 1AXg5998.t1, 4096; 1BXg5424.t1, 4528; 1AXg8556.t1, 4114;1BXg5433.t1, 4660 3AXg2591.t1, 2477; 1BXg5689.t1, 3AXg2961.t1, 4113;1BXg5696.t1, 3AXg6319.t1 4415; 3BXg1833.t1, 4503; 3BXg246.t1, 4501;3BXg3225.t1, 4369; 3BXg390.t1, 4498; 3BXg3977.t1, 4469; 3BXg443.t1,4495; 3BXg6039.t1, 4489; 3BXg8118.t1, 4394; 3BXg8171.t1, 44883BXg8955.t1 KEGG ko00520 Amino sugar none 2276; 1AXg10429.t1, 4101;1BXg11696.t1, 0.041684 PATHWAY and 2296; 608; 1AXg11997.t1, 2407;1BXg1175.t1, nucleotide 2294; 1AXg1785.t1, 4122; 1BXg1561.t1, sugar2287; 1AXg2013.t1, 2483; 1BXg2454.t1, metabolism 2284; 1AXg5017.t1,4120; 1BXg2483.t1, 2281; 1AXg5996.t1, 2382; 1BXg3531.t1, 2279;1AXg8113.t1, 2322; 1BXg3931.t1, 4559; 1AXg8814.t1, 4115; 1BXg4950.t1,4667; 3AXg10485.t1, 2350; 1BXg5592.t1, 4664; 3AXg2394.t1, 4105;1BXg9514.t1, 4662; 3AXg407.t1, 4408; 3BXg11985.t1, 4602 3AXg618.t1,4505; 3BXg2317.t1, 3AXg9481.t1 4502; 3BXg251.t1, 4410; 3BXg6843.t1,4362; 3BXg821.t1, 4486 3BXg9283.t1 KEGG ko00350 Tyrosine none 2275;1AXg11951.t1, 4098; 1BXg12278.t1, 0.045141 PATHWAY metabolism 1342;1AXg7766.t1, 4119; 1BXg2903.t1, 4609; 3AXg2591.t1, 4096; 1BXg5424.t1,4528; 3AXg2961.t1, 4113; 1BXg5696.t1, 4660 3AXg6319.t1 4108;1BXg8510.t1, 3185; 1BXg886.t1, 4415; 3BXg1833.t1, 4501; 3BXg3225.t1,4369; 3BXg390.t1, 4498; 3BXg3977.t1, 4495; 3BXg6039.t1, 4493;3BXg6827.t1, 4394; 3BXg8171.t1, 4488 3BXg8955.t1 KEGG ko00240 Pyrimidinenone 2274; 1AXg2750.t1, 2968; 1BXg1133.t1, 0.064093 PATHWAY metabolism1124; 662; 1AXg5630.t1, 2326; 1BXg4339.t1, 4648 1AXg7452.t1, 2352;1BXg5639.t1, 3AXg4651.t1 2463; 1BXg6885.t1, 4504 3BXg2357.t1

indicates data missing or illegible when filed

Gene Ontology Enrichment of Beneficial Fungi Versus Neutral Fungi

TABLE 707 GO enrichment of beneficial fungi versus neutral fungi GO SEQID SEQ ID FDR Term Description Beneficial A.Protein.ID NeutralB.Protein.ID q-value GO: 0005576 extracellular 478; 4917; 1AXg10805.t1,4926; 1BXg1054.t1, 1.82E−14 region 4918; 874; 1AXg1317.t1, 2435;1BXg11562.t1, 633; 2291; 1AXg21242.t1, 4101; 1BXg11696.t1, 2287; 2285;1AXg2815.t1, 4099; 1BXg12260.t1, 2284; 4947; 1AXg3175.t1, 4859;1BXg1692.t1, 2281; 667; 1AXg325.t1, 4927; 1BXg177.t1, 497; 4948;1AXg5017.t1, 4858; 1BXg2047.t1, 4877; 4919; 1AXg5538.t1, 2345;1BXg2053.t1, 4878; 4559; 1AXg5996.t1, 4928; 1BXg4311.t1, 4879; 4920;1AXg8019.t1, 4929; 1BXg4617.t1, 4515; 4880; 1AXg8113.t1, 4115;1BXg4950.t1, 4921; 4666; 1AXg9193.t1, 2377; 1BXg4998.t1, 4650; 4922;1AXg9750.t1, 4895; 1BXg6497.t1, 4923; 4881; 1AXg9874.t1, 4930;1BXg6576.t1, 4525; 4510; 3AXg10204.t1, 4896; 1BXg7924.t1, 4661; 4882;3AXg10215.t1, 4109; 1BXg8240.t1, 4924; 4925; 3AXg10410.t1, 2468;1BXg8760.t1, 4571; 4883; 3AXg10485.t1, 2721; 1BXg9114.t1, 4658; 46423AXg10796.t1, 4932; 3BXg10428.t1, 3AXg10814.t1, 4897; 3BXg10792.t1,3AXg10862.t1, 4356; 3BXg11001.t1, 3AXg2666.t1, 4898; 3BXg11147.t1,3AXg2755.t1, 4933; 3BXg11837.t1, 3AXg2790.t1, 4468; 3BXg12052.t1,3AXg2954.t1, 4934; 3BXg14356.t1, 3AXg5176.t1, 4351; 3BXg2216.t1,3AXg5370.t1, 4935; 3BXg2769.t1, 3AXg5893.t1, 4899; 3BXg3018.t1,3AXg5987.t1, 4900; 3BXg3920.t1, 3AXg6236.t1, 4386; 3BXg5319.t1,3AXg6314.t1, 4936; 3BXg5448.t1, 3AXg7257.t1, 4901; 3BXg6241.t1,3AXg7674.t1, 4428; 3BXg7066.t1, 3AXg8315.t1, 4902; 3BXg7579.t1,3AXg9121.t1, 4490; 3BXg7921.t1, 3AXg9736.t1, 4362; 3BXg821.t1,3AXg9876.t1, 4937; 3BXg9358.t1, 3AXg9889.t1 4442; 3BXg9632.t1, 49383BXg9781.t1 GO: 0008812 choline 4608; 4582; 3AXg1008.t1, 4387;3BXg1050.t1, 3.00E−06 dehydrogenase 4555; 4594; 3AXg10624.t1, 4365;3BXg3212.t1, activity 4562; 4829; 3AXg3404.t1, 4358; 3BXg4400.t1, 45603AXg3931.t1, 4811; 3BXg5049.t1, 3AXg6329.t1, 4363 3BXg7997.t13AXg8145.t1, 3AXg8514.t1 GO: 0005618 cell wall 4939; 614; 1AXg12959.t1,2413; 1BXg2549.t1, 1.22E−05 934; 4571; 1AXg2047.t1, 4475; 3BXg11145.t1,4940 1AXg6047.t1, 4341 3BXg3303.t1 3AXg9121.t1, 3AXg9980.t1 GO: 0016614oxidoreductase 4803; 4876; 1AXg11202.t1, 2433; 1BXg11481.t1, 2.62E−05activity, 4865; 4864; 1AXg1148.t1, 4857; 1BXg3389.t1, acting on 4863;4840: 1AXg7074.t1, 4844; 1BXg8979.t1, CH—OH 4527; 4518; 1AXg7314.t1,4843; 1BXg9251.t1, group of 4570; 4884; 1AXg8008.t1, 4824; 3BXg10091.t1,donors 4885; 4886; 3AXg10359.t1, 4466; 3BXg1035.t1, 4572; 4887;3AXg1658.t1, 4823; 3BXg10533.t1, 4888; 4538 3AXg2998.t1, 4479;3BXg13120.t1, 3AXg3962.t1, 4906; 3BXg3860.t1, 3AXg5234.t1, 4907;3BXg5594.t1, 3AXg5286.t1, 4908; 3BXg7349.t1, 3AXg6307.t1, 4909;3BXg7537.t1, 3AXg6312.t1, 4910; 3BXg8146.t1, 3AXg7030.t1, 4417;3BXg8641.t1, 3AXg7536.t1, 4399; 3BXg8643.t1, 3AXg8418.t1 49113BXg9353.t1 GO: 0000272 polysaccharide 2293; 2284; 1AXg2246.t1, 4125;1BXg10656.t1, 3.30E−05 catabolic 2273; 667; 1AXg5996.t1, 2435;1BXg11562.t1, process 1249; 4540; 1AXg6048.t1, 4101; 1BXg11696.t1, 4668;4941; 1AXg9193.t1, 2349; 1BXg2692.t1, 4923 1AXg9842.t1, 4928;1BXg4311.t1, 3AXg10237.t1, 2468; 1BXg8760.t1, 3AXg192.t1, 3093;1BXg9770.t1, 3AXg2760.t1, 4509; 3BXg10794.t1, 3AXg5370.t1 4356;3BXg11001.t1, 4343; 3BXg1101.t1, 4500; 3BXg3387.t1, 4942; 3BXg6628.t1,4423; 3BXg6890.t1, 4460 3BXg9765.t1 GO: 0045490 pectin 4948; 4666;1AXg9874.t1, 4099; 1BXg12260.t1, 3.30E−05 catabolic 4943; 45713AXg2790.t1, 4937; 3BXg9358.t1, process 3AXg5277.t1, 4449 3BXg9608.t13AXg9121.t1 GO: 0004252 serine-type 4804; 652; 1AXg11086.t1, 2467;1BXg10439.t1, 3.92E−05 endopeptidase 4947; 666; 1AXg7771.t1, 4850;1BXg782.t1, activity 4670; 4921; 1AXg8019.t1, 2452; 1BXg7838.t1, 4577;4834; 1AXg9261.t1, 4814; 3BXg1720.t1, 4922; 4525; 3AXg10865.t1, 4497;3BXg4508.t1, 4526 3AXg2755.t1, 4386; 3BXg5319.t1, 3AXg2995.t1, 4936;3BXg5448.t1, 3AXg3480.t1, 4355; 3BXg6263.t1, 3AXg5176.t1, 4944;3BXg6633.t1, 3AXg5987.t1, 4381; 3BXg8638.t1, 3AXg8810.t1 4485;3BXg9634.t1, 4945 3BXg9880.t1 GO: 0006979 response to 2272; 4626;1AXg6636.t1, 4103; 1BXg10186.t1, 1.11E−04 oxidative 4635 3AXg10815.t1,4860; 1BXg11947.t1, stress 3AXg2285.t1 4946 3BXg8947.t1 GO: 0030248cellulose 478; 4917; 1AXg10805.t1, 4926; 1BXg1054.t1, 1.51E−04 binding4918; 633; 1AXg1317.t1, 4927; 1BXg177.t1, 2291; 2287; 1AXg21242.t1,2345; 1BXg2053.t1, 2285; 2281; 1AXg3175.t1, 4929; 1BXg4617.t1, 497;4920; 1AXg325.t1, 4115; 1BXg4950.t1, 4924; 4925 1AXg5017.t1, 4930;1BXg6576.t1, 1AXg5538.t1, 4933; 3BXg11837.t1, 1AXg8113.t1, 4934;3BXg14356.t1, 1AXg9750.t1, 4935; 3BXg2769.t1, 3AXg10814.t1, 4428;3BXg7066.t1, 3AXg7674.t1, 4938 3BXg9781.t1 3AXg8315.t1 GO: 0016788hydrolase 4805; 4873; 1AXg10964.t1, 2489; 1BXg11282.t1, 3.35E−04activity, 496; 645; 1AXg1296.t1, 4862; 1BXg11329.t1, acting on 4836;4539; 1AXg13882.t1, 2445; 1BXg12241.t1, ester bonds 4569 1AXg13885.t1,2477; 1BXg5689.t1, 3AXg1785.t1, 4852; 1BXg6844.t1, 3AXg6767.t1, 4847;1BXg8700.t1, 3AXg8951.t1 4818; 3BXg12041.t1, 4467; 3BXg3959.t1, 4469;3BXg443.t1, 4905 3BXg5704.t1 GO: 0004190 aspartic-type 482; 494;1AXg10578.t1, 2439; 1BXg12089.t1, 3.46E−04 endopeptidase 673; 2252;1AXg6959.t1, 4853; 1BXg5763.t1, activity 4919; 4529; 1AXg6960.t1, 4076;1BXg6565.t1, 4833; 4581; 1AXg9542.t1, 2323; 1BXg7026.t1, 48943AXg10215.t1, 2474; 1BXg9737.t1, 3AXg1976.t1, 4842; 1BXg9738.t1,3AXg3738.t1, 4932; 3BXg10428.t1, 3AXg573.t1, 4347; 3BXg11695.t1,3AXg9318.t1 4472; 3BXg4394.t1, 4385; 3BXg5286.t1, 4483; 3BXg8935.t1,4904 3BXg9882.t1 GO: 0004650 polygalacturonase 4515; 4666; 3AXg10862.t1,2377; 1BXg4998.t1, 3.46E−04 activity 4943 3AXg2790.t1, 4937;3BXg9358.t1, 3AXg5277.t1 4442 3BXg9632.t1 GO: 0004185 serine-type 587;2282; 1AXg11050.t1, 4102; 1BXg10249.t1, 0.000484 carboxypeptidase 4838;4837; 1AXg7972.t1, 2386; 1BXg2887.t1, activity 4827; 4826; 3AXg10866.t1,4825; 3BXg10049.t1, 4624 3AXg1190.t1, 4812; 3BXg3887.t1, 3AXg891.t1,4353; 3BXg4014.t1, 3AXg9023.t1, 4432; 3BXg5175.t1, 3AXg9670.t1 4810;3BXg5715.t1, 4807 3BXg9635.t1 GO: 0016798 hydrolase 530; 2296;1AXg10268.t1, 4800; 1BXg10455.t1, 0.000484 activity, 4875; 477;1AXg11997.t1, 3811; 1BXg10918.t1, acting on 4872; 2292; 1AXg12212.t1,2483; 1BXg2454.t1, glycosyl 480; 2290; 1AXg13463.t1, 4949; 1BXg4330.t1,bonds 2289; 487; 1AXg15301.t1, 2352; 1BXg5639.t1, 4891; 4667;1AXg2742.t1, 4849; 1BXg817.t1, 4892; 4893 1AXg3149.t1, 2300;1BXg8757.t1, 1AXg3652.t1, 4813; 3BXg2207.t1, 1AXg3653.t1, 44803BXg8858.t1 1AXg5358.t1, 1AXg7786.t1, 3AXg2394.t1, 3AXg7003.t1,3AXg8007.t1 GO: 0005507 copper ion 4802; 1342; 1AXg12235.t1, 2539;1BXg10115.t1, 0.000489 binding 4632; 4597; 1AXg7766.t1, 4098;1BXg12278.t1, 4595; 4831 3AXg1263.t1, 4856; 1BXg3746.t1, 3AXg3686.t1,3185; 1BXg886.t1, 3AXg3946.t1, 4427; 3BXg10410.t1, 3AXg5094.t1 4817;3BXg12053.t1, 4403 3BXg689.t1 GO: 0008810 cellulase 4918; 1249;1AXg21242.t1, 4927; 1BXg177.t1, 0.000644 activity 4540; 4839;1AXg9842.t1, 4929; 1BXg4617.t1, 4941; 4532 3AXg10237.t1, 4930;1BXg6576.t1, 3AXg10372.t1, 4109; 1BXg8240.t1, 3AXg2760.t1, 3093;1BXg9770.t1, 3AXg6046.t1 4509; 3BXg10794.t1, 4343; 3BXg1101.t1, 4934;3BXg14356.t1, 4942; 3BXg6628.t1, 4903 3BXg9093.t1 GO: 0071555 cell wall4939; 614; 1AXg12959.t1, 4099; 1BXg12260.t1, 0.001751 organization 934;4515; 1AXg2047.t1, 2413; 1BXg2549.t1, 4666; 4659; 1AXg6047.t1, 2482;1BXg264.t1, 4940 3AXg10862.t1, 2377; 1BXg4998.t1, 3AXg2790.t1, 4475;3BXg11145.t1, 3AXg7872.t1, 4487; 3BXg928.t1, 3AXg9980.t1 4937;3BXg9358.t1, 4442 3BXg9632.t1 GO: 0008081 phosphoric 4520; 4950;3AXg3348.t1, 2343; 1BXg6110.t1, 0.003097 diester 4951 3AXg429.t1, 4952;3BXg10729.t1, hydrolase 3AXg8372.t1 4953; 3BXg10989.t1, activity 4954;3BXg1818.t1, 4388 3BXg5195.t1 GO: 0004601 peroxidase 4626; 46353AXg10815.t1, 2539; 1BXg10115.t1, 0.003136 activity 3AXg2285.t1 4808;3BXg8361.t1, 4946 3BXg8947.t1 GO: 0044238 primary 501; 4835;1AXg11043.t1, 4798 3BXg2943.t1 0.008701 metabolic 4630; 4830;3AXg3154.t1, process 4828 3AXg6318.t1, 3AXg8054.t1, 3AXg8258.t1 GO:0006629 lipid 4520; 4950; 3AXg3348.t1, 2339; 1BXg11161.t1, 0.022235metabolic 4832; 4951 3AXg429.t1, 2343; 1BXg6110.t1, process 3AXg4906.t1,4822; 3BXg10687.t1, 3AXg8372.t1 4952; 3BXg10729.t1, 4953; 3BXg10989.t1,4954; 3BXg1818.t1, 4388 3BXg5195.t1 GO: 0030246 carbohydrate 4801; 487;1AXg4233.t1, 4097; 1BXg135.t1, 0.022419 binding 4615 1AXg5358.t1, 4949;1BXg4330.t1, 3AXg4536.t1 4854; 1BXg5733.t1, 2332; 1BXg9970.t1, 4815;3BXg144.t1, 4422; 3BXg3121.t1, 4489; 3BXg8118.t1, 4484 3BXg9960.t1 GO:0008233 peptidase 567; 489; 1AXg1909.t1, 4124; 1BXg11338.t1, 0.026107activity 1013; 2286 1AXg3273.t1, 4861; 1BXg11861.t1, 1AXg3484.t1, 2858;1BXg2151.t1, 1AXg5534.t1 4846; 1BXg8705.t1, 4809 3BXg7109.t1 GO: 0016311dephosphorylation 485; 602; 1AXg1240.t1, 2329; 1BXg1583.t1, 0.0281094870; 4869; 1AXg12610.t1, 2401; 1BXg3489.t1, 4868; 4867; 1AXg2072.t1,4855; 1BXg4136.t1, 4866; 4841; 1AXg2679.t1, 4114; 1BXg5433.t1, 4889;4623; 1AXg3651.t1, 2478; 1BXg6623.t1, 4618; 4646; 1AXg5280.t1, 4821;3BXg10709.t1, 4890 1AXg7026.t1, 4439; 3BXg11186.t1, 3AXg10295.t1, 4816;3BXg12884.t1, 3AXg2325.t1, 4912; 3BXg23.t1, 3AXg2688.t1, 4503;3BXg246.t1, 3AXg6634.t1, 4913; 3BXg383.t1, 3AXg8755.t1, 4914;3BXg4227.t1, 3AXg9415.t1 4915; 3BXg5208.t1, 4425 3BXg5671.t1 GO: 0005886plasma 484; 4874; 1AXg11973.t1, 2336; 1BXg1674.t1, 0.120452 membrane4871; 649; 1AXg12543.t1, 2431; 1BXg3283.t1, 665; 658; 1AXg20005.t1,2451; 1BXg7238.t1, 651; 4641; 1AXg2148.t1, 4851; 1BXg7733.t1, 4521;4955; 1AXg4299.t1, 4848; 1BXg8189.t1, 4956; 4514; 1AXg4879.t1, 4845;1BXg8837.t1, 4957 1AXg9624.t1, 4820; 3BXg11471.t1, 3AXg10151.t1, 4819;3BXg11779.t1, 3AXg1507.t1, 4916; 3BXg11859.t1, 3AXg1833.t1, 44733BXg8700.t1 3AXg3620.t1, 3AXg7460.t1, 3AXg7667.t1 GO: 0008168methyltransferase 4799; 4663; 3AXg3246.t1, 4797; 3BXg5144.t1, 0.14079activity 4662 3AXg512.t1, 4492 3BXg7176.t1 3AXg618.t1

These data suggest that numerous biological processes are different inbeneficial endophytes, for example as compared to neutral endophytes.Some of these processes include cell wall degradation, starch andsucrose metabolism, and protection from oxidative stress.

One mechanism of entry of endophytes into intact plant tissue is byenzymatic processes involving degradation of cell walls. Beneficialendophytes used in this example show increased levels of secretedproteins that may be involved in such degradation, for example thosethat fall within the following gene ontology annotations: GO:0005618(cell wall), GO:0000272 (polysaccharide catabolic process), GO:0045490(pectin catabolic process), GO:0030248 (cellulose binding), GO:0004650(polygalacturonase activity), GO:0008810 (cellulase activity),GO:0071555 (cell wall organization), GO:0004185 (serine-typecarboxypeptidase activity), GO:0016798 (hydrolase activity, acting onglycosyl bonds), and GO:0030246 (carbohydrate binding). Certain of theproteins that fall within these gene ontology annotations may also beinvolved in starch and sucrose metabolism.

Beneficial endophytes of the invention secreted proteins that mayprovide a benefit to the plant, such as proteins involved in protectionagainst oxidative stress (GO:0016614 (oxidoreductase activity, acting onCH—OH group of donors); GO:0006979 (response to oxidative stress);GO:0005507 (copper ion binding), and GO:0004601 (peroxidase activity)).

Example 8: Greenhouse Characterization

Setup and Watering Conditions

A sandy loam growth substrate is mixed in the greenhouse and consistingof 60% loam and 40% mortar sand (Northeast Nursery, Peabody, Mass.).Prior to mixing, loam is sifted through a ⅜″ square steel mesh screen toremove larger particles and debris. Half of the appropriate fertilizersand soil treatments to be applied during the season is added to the soilmixture prior to sowing. The remaining components are provided dissolvedin irrigation water at the onset of the reproductive stages ofdevelopment. Substrate surface area per pot is calculated based on potdiameter in order to approximate the “acreage” of individual pots. Anequivalent volume of fertilized soil is then gently added to each pot inorder to minimize compaction of the soil. The substrate is saturatedwith water 3-4 hours before sowing.

Commercially available seeds (e.g., seeds described herein) are coatedwith microbial treatments using the formulation used for field trialsand described herein. Treatments included microbial coatings and twocontrols (non-treated and formulation). Three seeds are sown evenlyspaced at the points of a triangle. Soil is then overlaid atop the seedsand an additional 200 mL water was added to moisten the overlayingsubstrate.

Midseason Measurements and Harvest

Emergence percentage is observed. Further, at various times through thegrowing season, plants are assessed for onset of and recovery fromstress symptoms, for example but not limited to: leaf senescence,anthesis-silking interval, leaf chlorophyll content, grain weight, andtotal yield.

To compare treated plants to controls, a fully Bayesian robust t-test isperformed. Briefly, R (R Core Team, 2015) was used with the BEST package(Kruschke and Meredith, 2015) and JAGS (Plummer, 2003) to perform aMarkov Chain Monte Carlo estimation of the posterior distribution thelikely differences between the two experimental groups. A 95% highestdensity interval (HDI) is overlayed onto this distribution to aid in theinterpretation of whether the two biological groups truly differ.

Tissue Collection and Processing for Transcriptomics, Hormone, andMetabolomics Analysis

In order to assess the effects of endophyte treatment on plant growth atthe transcriptomic, phytohormone, and metabolomic levels, plants areharvested. Three pots from each treatment are selected. Once separated,the tissues (roots, stems, leaves, other plant elements as appropriate)from the three pots of each treatment are pooled. For collection, firstall loosely attached substrate is removed from the roots by gentlytapping and shaking the roots. Any adherent substrate is removed bysubmerging the roots in water and manually dislodging attached soil anddebris. The roots are then blotted dry before being cut from the aerialtissue, followed by separating petioles and leaves from the stem. Astissues are removed from the plant they are immediately bagged andfrozen in liquid nitrogen. All harvested tissues are kept in liquidnitrogen or stored at −80° C. until further processing.

To prepare for analyses, the tissues are ground with liquid nitrogenusing a pre-chilled mortar and pestle. Approximately 100-200 microgramsof each ground sample pool is transferred to a chilled 1.5 mL microtubefor RNA extraction and subsequent transcriptome, phytohormone andmetabolite analysis. For proteomic analysis, 3 g of each ground samplepool is used. The remaining ground tissue is then transferred to achilled 50 mL conical tube and stored in liquid nitrogen or at −80° C.until shipment for further analyses.

Example 9: Assessment of Plant Colonization

The protocols described in this section allow confirmation of successfulcolonization of plants by endophytes, for example by direct recovery ofviable colonies from various tissues of the inoculated plant.

Recovery of Viable Colonies from Seeds

Seeds are surface-sterilized by exposing them to chlorine gas overnight,using the methods described elsewhere. Sterile seeds are then inoculatedwith submerged in 0.5 OD overnight cultures (Tryptic Soy Broth, TSB) ofbacteria and allowed to briefly air dry. The seeds are then placed intubes filled partially with a sterile sand-vermiculite mixture [(1:1wt:wt)] and covered with 1 inch of the mixture, watered with sterilewater, sealed and incubated in a greenhouse for 7 days. Afterincubation, various tissues of the plants are harvested and used asdonors to isolate bacteria by placing tissue section in a homogenizer(TSB 20%) and mechanical mixing. The slurry is then serially diluted in10-fold steps to 10-3 and dilutions 1 through 10-3 are plated on TSA 20%plates (1.3% agar). Plates are incubated overnight and pictures aretaken of the resulting plates as well as colony counts for CFU. Bacteriaare identified visually by colony morphotype and molecular methodsdescribed herein. Representative colony morphotypes are also used incolony PCR and sequencing for isolate identification via ribosomal genesequence analysis as described herein. These trials are repeated twiceper experiment, with 5 biological samples per treatment.

Culture-Independent Methods to Confirm Colonization of the Plant orSeeds by Bacteria or Fungi

One way to detect the presence of endophytes on or within plants orseeds is to use quantitative PCR (qPCR). Internal colonization by theendophyte can be demonstrated by using surface-sterilized plant tissue(including seed) to extract total DNA, and isolate-specific fluorescentMGB probes and amplification primers are used in a qPCR reaction. Anincrease in the product targeted by the reporter probe at each PCR cycletherefore causes a proportional increase in fluorescence due to thebreakdown of the probe and release of the reporter. Fluorescence ismeasured by a quantitative PCR instrument and compared to a standardcurve to estimate the number of fungal or bacterial cells within theplant.

Experimental Description

The design of both species-specific amplification primers, andisolate-specific fluorescent probes are well known in the art. Planttissues (seeds, stems, leaves, flowers, etc.) are pre-rinsed and surfacesterilized using the methods described herein.

Total DNA is extracted using methods known in the art, for example usingcommercially available Plant-DNA extraction kits, or the followingmethod.

1. Tissue is placed in a cold-resistant container and 10-50 mL of liquidnitrogen is applied. Tissues are then macerated to a powder.

2. Genomic DNA is extracted from each tissue preparation, following achloroform:isoamyl alcohol 24:1 protocol (Sambrook et al., 1989).

Quantitative PCR is performed essentially as described by Gao et al.(2010) with primers and probe(s) specific to the desired isolate using aquantitative PCR instrument, and a standard curve is constructed byusing serial dilutions of cloned PCR products corresponding to thespecie-specific PCR amplicon produced by the amplification primers. Dataare analyzed using instructions from the quantitative PCR instrument'smanufacturer software.

As an alternative to qPCR, Terminal Restriction Fragment LengthPolymorphism, (TRFLP) can be performed, essentially as described inJohnston-Monje and Raizada (2011). Group specific, fluorescentlylabelled primers are used to amplify a subset of the microbialpopulation, especially bacteria, especially fungi, especially archaea,especially viruses. This fluorescently labelled PCR product is cut by arestriction enzyme chosen for heterogeneous distribution in the PCRproduct population. The enzyme cut mixture of fluorescently labelled andunlabeled DNA fragments is then submitted for sequence analysis on aSanger sequence platform such as the Applied Biosystems 3730 DNAAnalyzer.

Immunological Methods to Detect Microbes in Seeds and Vegetative Tissues

A polyclonal antibody is raised against specific bacteria X or fungus Ystrains via standard methods. A polyclonal antibody is also raisedagainst specific GUS and GFP proteins via standard methods.Enzyme-linked immunosorbent assay (ELISA) and immunogold labeling isalso conducted via standard methods, briefly outlined below.

Immunofluorescence microscopy procedures involve the use of semi-thinsections of plant element or adult plant tissues transferred to glassobjective slides and incubated with blocking buffer (20 mM Tris(hydroxymethyl)-aminomethane hydrochloride (TBS) plus 2% bovine serumalbumin, pH 7.4) for 30 min at room temperature. Sections are firstcoated for 30 min with a solution of primary antibodies and then with asolution of secondary antibodies (goat anti-rabbit antibodies) coupledwith fluorescein isothiocyanate (FITC) for 30 min at room temperature.Samples are then kept in the dark to eliminate breakdown of thelight-sensitive FITC. After two 5-min washings with sterile potassiumphosphate buffer (PB) (pH 7.0) and one with double-distilled water,sections are sealed with mounting buffer (100 mL 0.1 M sodium phosphatebuffer (pH 7.6) plus 50 mL double-distilled glycerine) and observedunder a light microscope equipped with ultraviolet light and a FITCTexas-red filter.

Ultrathin (50- to 70-nm) sections for TEM microscopy are collected onpioloform-coated nickel grids and are labeled with 15-nm gold-labeledgoat anti-rabbit antibody. After being washed, the slides are incubatedfor 1 h in a 1:50 dilution of 5-nm gold-labeled goat anti-rabbitantibody in IGL buffer. The gold labeling is then visualized for lightmicroscopy using a BioCell silver enhancement kit. Toluidine blue(0.01%) is used to lightly counterstain the gold-labeled sections. Inparallel with the sections used for immunogold silver enhancement,serial sections are collected on uncoated slides and stained with 1%toluidine blue. The sections for light microscopy are viewed under anoptical microscope, and the ultrathin sections are viewed by TEM.

Example 10: Assessment of Improved Plant Characteristics: DifferentiallyRegulated Hormones

Methods

For hormone analysis, 100±10 mg tissue is measured into microtubes(chilled with liquid nitrogen), and sent on dry ice to a vendor. Planthormone analysis is performed per Christiansen et al. (2014) with slightmodification. Briefly, hormones are extracted from 100±10 mg of frozentissue and tissue weights are recorded for quantification. A mixturecontaining 10 microliters of 2.5 microMolar internal standards and 500microliters of extraction buffer [1-propanol/H2O/concentrated HCl(2:1:0.002, vol/vol/vol) is added to each sample and vortexed untilthawed. Samples are agitated for 30 min at 4° C., then 500 microlitersof dichloromethane (CH2Cl2) is added. Samples are agitated again for 30min at 4° C., and then centrifuged at 13,000×g for 5 min. in darkness.The lower organic layer is removed into a glass vial and the solvent isevaporated by drying samples for 30-40 min under a N2 stream. Samplesare re-solubilized in 150 microliters of MeOH, shaken for 1 min andcentrifuged at 14,000×g for 2 min. A supernatant of 90 microliters istransferred into the autosampler vial and hormones are analyzed byultraperformance liquid chromatography, coupled to mass spectrometry(UPLC-MS/MS). Ascentis Express C-18 Column (3 cm×2.1 mm, 2.7 cm) isconnected to an API 3200 using electrospray ionization-tandem massspectrometry (MS/MS) with scheduled multiple reaction monitoring (SMRM).The injection volume is 5 microliters and has a 300 microliters/minmobile phase consisting of Solution A (0.05% acetic acid in water) andSolution B (0.05% acetic acid in acetonitrile) with a gradientconsisting of (time-% B): 0.3-1%, 2-45%, 5-100%, 8-100%, 9-1%, 11-stop.Quantitation is carried out with Analyst software (AB Sciex), using theinternal standards as a reference for extraction recovery. Leaf, root,and/or other tissue is saved in −62° C. and saved for subsequent geneexpression analysis.

Mass spectra of plant hormones are obtained. Fold changes betweencontrol and treated samples are calculated by dividing the mass spectrumvalue from the treated sample by the value from the control sample.

Modulation of hormones related to growth as well as related toresistance to abiotic and biotic stresses are found in plants treatedwith endophytes as compared to isoline plants lacking such treatment.

Example 11: Assessment of Improved Plant Characteristics andDifferentially Regulated Metabolites

Methods

For metabolite analysis, 150±10 mg of each sample is transferred into1.5 mL microtubes (chilled in liquid nitrogen) and sent on dry ice tothe Proteomics and Metabolomics Facility at Colorado State University.Metabolomics data acquisition is performed per the following methodsprovided by Dr. Corey Broeckling at CSU. To prepare the samples foranalysis, phytohormones are extracted from ground plant material using abiphasic protocol. One mL of a methyl tert-butyl ether (MTBE):methanol:water mixture (6:3:1) is added to each sample then shaken for 1hour. Next, 250 microliters cold water and a mix of internal standardsare added to each sample to promote phase separation. Samples are shakenagain for 5 minutes. Samples are then centrifuged at 2,095×g at 4° C.for 15 minutes. The organic top phase is removed for hormone analysis,dried under an inert nitrogen environment, then re-suspended in 400microliters of 50% acetonitrile. Extracts are then directly analyzed byLC-MS.

For GC-MS, the polar (lower phase) extract is dried using a speedvac,resuspended in 50 microliters of pyridine containing 50 mg/mL ofmethoxyamine hydrochloride, incubated at 60° C. for 45 min, sonicatedfor 10 min, and incubated for an additional 45 min at 60° C. Next, 25microliters of N-methyl-N-trimethylsilyltrifluoroacetamide with 1%trimethylchlorosilane (MSTFA+1% TMCS, Thermo Scientific) is added andsamples re incubated at 60° C. for 30 min, centrifuged at 3000×g for 5min, cooled to room temperature, and 80 microliters of the supernatantis transferred to a 150 microliters glass insert in a GC-MS autosamplervial. Metabolites are detected using a Trace GC Ultra coupled to aThermo ISQ mass spectrometer (Thermo Scientific). Samples are injectedin a 1:10 split ratio twice in discrete randomized blocks. Separationoccurs using a 30 m TG-5MS column (Thermo Scientific, 0.25 mm i.d., 0.25micrometer film thickness) with a 1.2 mL/min helium gas flow rate, andthe program consists of 80° C. for 30 sec, a ramp of 15° C. per min to330° C., and an 8 min hold. Masses between 50-650 m/z re scanned at 5scans/sec after electron impact ionization. The ionization source iscleaned and retuned and the injection liner replaced between injectionreplicates. Analysis for plant hormones is performed by UPLC-MS/MS asfollows.

Metabolites are detected and mass spectra annotated by comparing tolibraries of known spectra including an in-house database at CSU (LC-MSonly), the National Institute of Standards and Technology databases,Massbank MS database, and the Golm Metabolite Database. Initialannotation is automated, followed by manual validation of annotations.Following annotation, compounds are identified. After removal oftechnical artifacts (e.g. siloxane), and ambiguous or vague annotations(e.g. carbohydrate or saccharide), identified compounds remain foranalysis. These compounds are assessed for fold change over controlplants. Metabolites are grouped by pathways (e.g. carbohydratemetabolism or alkaloid biosynthesis) and the KEGG database andliterature are manually referenced to identify pertinent shifts inmetabolic patterns in plants treated with microbes. Any compound withoutan appreciable shift compared to that observed in control plants isremoved from further analysis.

Modulation of metabolites related to growth as well as related toresistance to abiotic and biotic stresses are found in plants treatedwith endophytes as compared to isoline plants lacking such treatment.

Example 12: Efficacy Testing of Endophytes in Crop Production

Method

Whole plants or plant elements, such as seeds, roots, or leaves, fromany of the crops useful in the invention are treated with endophytes asdescribed in Examples 3, 4, or 8. They are then sown in a variety indifferent growing regions for efficacy testing. Trials consist of tenreplicate plots for each treatment and control respectively arranged ina spatially balanced randomized complete block design (Van Es et al.2007). In addition to measuring total yield, metrics such as seedlingemergence, normalized difference vegetation index (NDVI) and time toflowering are assessed. Endophytes are applied alone as a seedtreatment, as well as in combination with other endophytes.

Results

Crop plants that have been treated with the endophyte(s) of the presentinvention demonstrate improvements in one or moreagronomically-important characteristic, for example but not limited to:disease resistance, drought tolerance, heat tolerance, cold tolerance,salinity tolerance, metal tolerance, herbicide tolerance, chemicaltolerance, improved water use efficiency, improved nitrogen utilization,improved nitrogen fixation, pest resistance, herbivore resistance,pathogen resistance, increased yield, increased yield underwater-limited conditions, health enhancement, vigor improvement, growthimprovement, photosynthetic capability improvement, nutritionenhancement, altered protein content, altered oil content, increasedbiomass, increased shoot length, increased root length, improved rootarchitecture, improved plant standability, increased plant elementweight, altered plant element carbohydrate composition, altered plantelement oil composition, number of pods, delayed senescence, stay-green,and altered plant element protein composition.

Example 13: Generating/Isolating Endophytes Compatible withAgrochemicals

The application of pesticides against fungal pathogens ofagriculturally-relevant plants is a common practice in agriculture toensure higher yields. One method of pesticide delivery is to cover theseeds with a coating with pesticides. Although pesticides are meant todeter the growth and propagation of pathogenic microorganisms, they mayalso affect endophyte populations residing inside of the seed. For thispurpose, conferring compatibility mechanisms to endophytic fungiproviding beneficial properties which are sensitive to these compoundsis desirable for the maintenance of endophytes in the seeds.

Compatibility with pesticides can be intrinsic (naturally pesticidecompatible fungi, for example) or acquired (due to mutations in thegenetic material of the microorganism, or to the introduction ofexogenous DNA by natural DNA transfer).

Fungicides used as protectants are effective only on the seed surface,providing protection against seed surface-borne pathogens and providingsome level of control of soil-borne pathogens. These products generallyhave a relatively short residual. Protectant fungicides such as captan,maneb, thiram, or fludioxonil help control many types of soil-bornepathogens, except root rotting organisms. Systemic fungicides areabsorbed into the emerging seedling and inhibit or kill susceptiblefungi inside host plant tissues. Systemic fungicides used for seedtreatment include the following: azoxystrobin, carboxin, mefenoxam,metalaxyl, thiabendazole, trifloxystrobin, and various triazolefungicides, including difenoconazole, ipconazole, tebuconazole, andtriticonazole. Mefenoxam and metalaxyl are primarily used to target theoomycetes such as species of Pythium and Phytophthora.

Strobilurin analogues, such as azoxystrobin, inhibit mitochondrialrespiration by blocking electron transfer at the cytochrome bcl complex.Phenylamides, including metalaxyl, interfere with RNA synthesis intarget fungi. Oxathiin systemic fungicides like carboxin inhibits theincorporation of phenylalanine into protein and of uracil into RNA.Azole fungicides BAS 480F, flusilazole, and tebuconazole are inhibitorsof sterol 14a-demethylase, and block sterol biosynthesis.

I. Determination of Intrinsic Resilience Against Agrochemicals ofBacteria Cultured from Seeds

To test the intrinsic resilience pesticides of bacteria isolated asdescribed herein, minimum inhibitory concentration (MIC) assays areperformed on all isolated bacteria of interest, as described in Wiegand,Irith, Kai Hilpert, and Robert E W Hancock. Nature protocols 3.2 (2008):163-175, which is incorporated herein by reference in its entirety.Briefly, known concentrations of bacterial cells or spores are used toinoculate plates containing solid media with different concentrations ofthe pesticide, or to inoculate liquid media containing differentconcentrations of the pesticide (in a 96-well plate). The pesticides areused at the concentration recommended by the manufacturer for seedcoating, and two-fold dilutions down to 0.000125 (12 two-folddilutions). Growth is assessed after incubation for a defined period oftime (16-20 h) and compared to cultures grown in the same manner withoutany pesticides as control. The MIC value is determined as described inWiegand, Irith, Kai Hilpert, and Robert E W Hancock. Nature protocols3.2 (2008): 163-175.

II. Determination of Intrinsic Resilience Against Agrochemicals of FungiCultured from Seeds

To test the intrinsic resilience against pesticides of the fungiisolated as described in this application, minimum inhibitoryconcentration (MIC) assays are performed on all isolated fungi ofinterest, as described in Mohiddin, F. A., and M. R. Khan. AfricanJournal of Agricultural Research 8.43 (2013): 5331-5334 (incorporatedherein by reference in its entirety), with the following changes:Briefly, double strength potato dextrose agar is prepared containingdifferent concentrations of each pesticide. The pesticides are appliedat the concentration recommended by the manufacturer, and also in twofold dilutions to 0.000125× (12 two-fold dilutions). Thereafter, theplates are seeded centrally with a 3 mm disc of 4 days old culture ofeach fungus that had been centrifuged and rinsed twice in sterilephosphate buffer. PDA plates without a fungicide but inoculated with thefungi serve as a control. The inoculated plates are incubated at 25±2°C. for 5 days. The radial growth of the colony in each treatment ismeasured and the percent inhibition of growth is calculated as describedby Mohiddin, F. A., and M. R. Khan. African Journal of AgriculturalResearch 8.43 (2013): 5331-5334 (incorporated herein by reference in itsentirety). Fungal isolates are classified as resilience against theparticular pesticide if their maximum tolerance concentration (MTC) is2x or above the concentration of pesticides recommended to be used inseed coatings.

III. Generating Fungal Species with Compatibility with CommercialPesticides Coated onto Seeds

When a fungal strain of interest that provides a beneficial property toits plant host is found to be sensitive to a commercially-relevantpesticide, pesticide-compatible variants of the strains need to begenerated for use in this application. Generation of compatibility tomultiple pesticides or cocktails of pesticides is accomplished bysequentially selecting compatible variants to each individual pesticideand then confirming compatibility with a combination of the pesticides.After each round of selection, fungi are tested for their ability toform symbiotic relationships with the plants and to confirm that theyprovide a beneficial property on the plant as did the parental strain,with or without application of the pesticide product as describedherein.

Generation and isolation of pesticide-compatible strains derived fromendophytic strains isolated from seeds and shown to provide beneficiarytraits to plants is performed as described by Shapiro-Ilan, David I., etal. Journal of invertebrate pathology 81.2 (2002): 86-93 (incorporatedherein by reference in its entirety), with some changes. Briefly, sporesof the isolated fungi are collected and solutions containing between1×103 spores are used to inoculate potato dextrose agar (PDA) platescontaining 2, 5, and 10 times the MTC of the particular strain. Platesare incubated for 1-5 days and a single colony from the highestconcentration of pesticide which allows growth is inoculated onto afresh plate with the same pesticide concentration 7 consecutive times.After compatibility has been established, the strain is inoculated ontoPDA plates 3 consecutive times and then inoculated onto a PDA platecontaining the pesticide to confirm that the compatibility trait ispermanent.

Alternatively, if this method fails to provide a compatible strain, aspore suspension is treated with ethyl methanesulfonate to generaterandom mutants, similarly as described by Leonard, Cory A., Stacy D.Brown, and J. Russell Hayman. International journal of microbiology 2013(2013), Article ID 901697 (incorporated herein by reference in itsentirety) and spores from this culture are used in the experimentdetailed above.

To develop fungal endophytes compatible with multiple pesticides orcocktails of pesticides, spores of a strain compatible with one or morepesticides are used to select for variants to a new pesticide asdescribed above. Strains developed this way are tested for retention ofthe pesticide-compatibility traits by inoculating these strains onto PDAplates containing each single pesticide or combinations of pesticides.

IV. Generating Bacterial Species with Compatibility to CommercialPesticides Coated onto Seeds

When a bacterial strain of interest is found to be sensitive to acommercially-relevant pesticide, generation of pesticide-compatiblevariants of the strains can be generated for use in this application.Generation of compatible with multiple pesticides or cocktails ofpesticides is accomplished by first sequentially selecting variantscompatible with incrementally higher concentrations of each individualpesticide (as described by Thomas, Louise, et al. Journal of HospitalInfection 46.4 (2000): 297-303, which is incorporated herein byreference in its entirety). To develop bacterial endophytes compatiblewith multiple pesticides or cocktails of pesticides, bacterial cells ofa strain compatible with one or more pesticides is used to select forvariants to a new pesticide as described above. Strains developed thisway are tested for retention of the pesticide-compatible traits byinoculating these strains onto PDA plates containing each singlepesticide or combinations of pesticides.

After each round of selection, bacteria are tested for their ability tolive within plants and for their ability to provide the same beneficialproperty to the plant as did the parental strain, with or withoutapplication of the pesticide product to the plants as described herein.

V. Generation of Pesticide-Compatible Bacteria by Insertion of aResistance Plasmid

Many bacterial plasmids that confer compatible pesticides have beendescribed in the literature (Don, R. H., and J. M. Pemberton. Journal ofBacteriology 145.2 (1981): 681-686; and Fisher, P. R., J. Appleton, andJ. M. Pemberton. Journal of bacteriology 135.3 (1978): 798-804, each ofwhich is incorporated herein by reference in its entirety)

For cases in which obtaining naturally occurring compatible bacteria isnot feasible, use of these plasmids is a possible way to developendophytic strains compatible with multiple pesticides.

For example, a Pseudomonas fluorescens strain that providesanti-nematode properties to plants but is sensitive to the pesticides2,4-dichlorophenoxyacetic acid and 4-chloro-2-methylphenoxyacetic can betransformed with the plasmid pJP2 (isolated from Alcaligenes eutrophus)which provides transmissible compatible with these compounds, asdescribed by Don and Pemberton, 1981. Briefly, plasmids are transferredby conjugation to Pseudomonas, using the method described in Haas,Dieter, and Bruce W. Holloway. Molecular and General Genetics 144.3(1976): 243-251 (incorporated herein by reference in its entirety).

After the generation of bacteria carrying pesticide-compatibilityconferring plasmids, these endophytes are tested for their ability tolive inside plant tissues and for their ability to provide the samebeneficial property to the plant as it did for the parental strain, withor without application of the pesticide product to the plants asdescribed herein.

VI. Growth and Scale-Up of Bacteria for Inoculation on Solid Media

The bacterial isolates are grown by loop-inoculation of a single colonyinto R2A broth (supplemented with appropriate antibiotics) in 100 mLflasks. The bacterial culture is incubated at 30±2 OC for 2 days at 180rpm in a shaking incubator (or under varying temperatures and shakingspeeds as appropriate). This liquid suspension is then used to inoculateheat sterilized vermiculite powder that is premixed with sterile R2Abroth (without antibiotics), resulting in a soil like mixture ofparticles and liquid. This microbial powder is then incubated for anadditional couple of days at 30±2 OC with daily handshaking to aeratethe moist powder and allow bacterial growth. Microbially inoculatedvermiculite powder is now ready for spreading on to soil or onto plantparts. Alternatively, the R2A broth is used to inoculate Petri dishescontaining R2A or another appropriate nutrient agar where lawns ofbacteria are grown under standard conditions and the solid coloniesscraped off, resuspended in liquid and applied to plants as desired.

VII. Growth & Scale-Up of Fungi for Inoculation on Solid Media

Once a fungal isolate has been characterized, conditions are optimizedfor growth in the lab and scaled-up to provide sufficient material forassays. For example, the medium used to isolate the fungus issupplemented with nutrients, vitamins, co-factors, plant-extracts, andother supplements that can decrease the time required to grow the fungalisolate or increase the yield of mycelia and/or spores the fungalisolate produces. These supplements can be found in the literature orthrough screening of different known media additives that promote thegrowth of all fungi or of the particular fungal taxa.

To scale up the growth of fungal isolates, isolates are grown from afrozen stock on several Petri dishes containing media that promotes thegrowth of the particular fungal isolate and the plates are incubatedunder optimal environmental conditions (temperature, atmosphere, light).After mycelia and spore development, the fungal culture is scraped andresuspended in 0.05M Phosphate buffer (pH 7.2, 10 mL/plate). Disposablepolystyrene Bioassay dishes (500 cm2, Thermo Scientific NuncUX-01929-00) are prepared with 225 mL of autoclaved media with anyrequired supplements added to the media, and allowed to solidify. Platesare stored at room temperature for 2-5 days prior to inoculation toconfirm sterility. 5 mL of the fungal suspension is spread over thesurface of the agar in the Bioassay plate in a biosafety cabinet, platesare allowed to dry for 1h, and they are then incubated for 2-5 days, oruntil mycelia and/or spores have developed.

A liquid fungal suspension is then created via the following. Fungalgrowth on the surface of the agar in the Bioassay plates are thenscraped and resuspended in 0.05M Phosphate buffer (pH 7.2). OD600readings are taken using a spectrometer and correlated to previouslyestablished OD600/CFU counts to estimate fungal population densities,and the volume adjusted with additional sodium phosphate buffer toresult in 100 mL aliquots of fungi at a density of approximately106-1011 spores/mL. This suspension may or may not be filtered to removemycelia and can be used to create a liquid microbial formulation asdescribed herein to apply the fungal isolate onto a plant, plant part,or seed.

VIII. Growth & Scale-Up of Bacteria for Inoculation in Liquid Media

Bacterial strains are grown by loop-inoculation of one single colonyinto R2A broth (amended with the appropriate antibiotics) in 100 mLflasks. The bacterial culture is incubated at 28±2 OC for 1 day at 180rpm in a shaking incubator (or under varying temperatures and shakingspeeds as appropriate). The bacteria are pelleted by centrifugation andresuspended in sterile 0.1 M sodium phosphate. OD600 readings are takenusing a spectrometer and correlated to previously established OD600/CFUcounts to estimate bacterial population densities, and the volumeadjusted with additional sodium phosphate buffer to result in 100 mLaliquots of bacteria at a density of 1×108 cells/mL. To help breaksurface tension, aid bacterial entry into plants and provide microbesfor some energy for growth, 10 μL of Silwet L-77 surfactant and 1 g ofsucrose is added to each 100 mL aliquot (resulting in 0.01% v/v and 1%v/v concentrations, respectively) in a similar way as in the protocolfor Agrobacterium-mediated genetic transformation of Arabidopsisthaliana seed [Clough, S., Bent, A. (1999) The Plant Journal 16(6):735-743].

IX. Growth & Scale-Up of Fungi for Inoculation in Liquid Media

Once a fungal isolate has been characterized, conditions are optimizedfor growth in the lab and scaled-up to provide enough material forassays. For example, the medium used to isolate the fungi issupplemented with nutrients, vitamins, co-factors, plant-extracts,and/or other supplements that can decrease the time required to grow thefungal isolate and/or increase the yield of mycelia and/or spores thefungal isolate produces. These supplements can be found in theliterature or through screening of different known media additives thatpromote the growth of all fungi or of the particular fungal taxa.

To scale up the growth of fungal isolates, isolates are grown from afrozen stock on Petri dishes containing media that promotes the growthof the particular fungal isolate and the plates are incubated underoptimal environmental conditions (temperature, atmosphere, light). Aftermycelia and spore development, the fungal culture is scraped andresuspended in 0.05M Phosphate buffer (pH 7.2, 10 mL/plate). 1 liter ofliquid media selected to grow the fungal culture is prepared in 2 Lglass flasks and autoclaved and any required supplements added to themedia. These are stored at room temperature for 2-5 days prior toinoculation to confirm sterility. 1 mL of the fungal suspension is addedaseptically to the media flask, which is then incubated for 2-5 days, oruntil growth in the liquid media has reached saturation. Spore countsare determined using hemacytometer and correlated to previouslyestablished OD600/CFU counts to estimate fungal population densities,and the volume adjusted with additional sodium phosphate buffer toresult in 100 mL aliquots of fungi at a density of approximately106-1011 spores/mL. This suspension may or may not be filtered to removemycelia and can be used to create a liquid microbial formulation asdescribed herein to apply the fungal isolate onto a plant, plant part,or seed.

X. Creation of Liquid Microbial Formulations or Preparations for theApplication of Microbes to Plants

Bacterial or fungal cells are cultured in liquid nutrient broth mediumto between 102-1012 CFU/mL. The cells are separated from the medium andsuspended in another liquid medium if desired. The microbial formulationmay contain one or more bacterial or fungal strains. The resultingformulation contains living cells, lyophilized cells, or spores of thebacterial or fungal strains. The formulation may also contain water,nutrients, polymers and binding agents, surfactants or polysaccharidessuch as gums, carboxymethylcellulose and polyalcohol derivatives.Suitable carriers and adjuvants can be solid or liquid and includenatural or regenerated mineral substances, solvents, dispersants,wetting agents, tackifiers, thickeners, binders or fertilizers.Compositions can take the form of aqueous solutions, oil-in-wateremulsions, or water-in-oil emulsions. Small amounts of insolublematerial can optionally be present, for example in suspension in themedium, but it is generally preferred to minimize the presence of suchinsoluble material.

XI. Inoculation of Plants by Coating Microbes Directly onto Seed

Seed is treated by coating it with a liquid microbial formulation(prepared as described herein) comprising microbial cells and otherformulation components, directly onto the seed surface at the rate of102-108 microbial CFU per seed. Seeds are soaked in liquid microbialformulation for 1, 2, 3, 5, 10, 12, 18 or 24 hours or 2, 3, or 5 days.After soaking in microbial formulation, seeds are planted in growingcontainers or in an outdoor field. Seeds may also be coated with liquidmicrobial formulation by using an auger or a commercial batch treater.One or more microbial formulations or other seed treatments are appliedconcurrently or in sequence. Treatment is applied to the seeds using avariety of conventional treatment techniques and machines, such asfluidized bed techniques, augers, the roller mill method, rotostaticseed treaters, and drum coaters. Other methods, such as spouted beds mayalso be useful. The seeds are pre-sized before coating. Optionally themicrobial formulation is combined with an amount of insecticide,herbicide, fungicide, bactericide, or plant growth regulator, or plantmicro- or macro-nutrient prior to or during the coating process. Aftercoating, the seeds are typically dried and then transferred to a sizingmachine for grading before planting. Following inoculation, colonizationof the plants or seeds produced therefrom is confirmed via any of thevarious methods described herein. Growth promotion or stress resiliencebenefits to the plant are tested via any of the plant growth testingmethods described herein.

XII. Inoculation of Plants with a Combination of Two or More Microbes

Seeds can be coated with bacterial or fungal endophytes. This methoddescribes the coating of seeds with two or more bacterial or fungalstrains. The concept presented here involves simultaneous seed coatingof two microbes (e.g., both a gram negative endophytic bacteriumBurkholderia phytofirmans and a gram positive endophytic bacteriumBacillus mojavensis). Optionally, both microbes are geneticallytransformed by stable chromosomal integration as follows. Bacillusmojavensis are transformed with a construct with a constitutive promoterdriving expression of a synthetic operon of GFPuv and spectinomycinresistance genes, while Burkholderia phytofirmans are transformed with aconstruct with a constitutive promoter driving expression of the lacoperon with an appended spectinomycin resistance gene. Seeds are coatedwith a prepared liquid formulation of the two microbes the variousmethods described herein. Various concentrations of each endophyte inthe formulation is applied, from 102 CFU/seed to about 108 CFU/seed.Following inoculation, colonization of the plants or seeds producedtherefrom may be confirmed via any of the various methods describedherein. Growth promotion or stress resilience benefits to the plant aretested via any of the plant growth testing methods described herein.

XIII. Culturing to Confirm Colonization of Plant by Bacteria

The presence in the seeds or plants of GFPuv or gusA-labeled endophytescan be detected by colony counts from mashed seed material andgerminated seedling tissue using R2A plates amended with5-Bromo-4-chloro-3-indolyl β-D-glucuronide (X-glcA, 50 μg/mL), IPTG (50μg/mL) and the antibiotic spectinomycin (100 μg/mL). Alternatively,bacterial or fungal endophytes not having received transgenes can alsobe detected by isolating microbes from plant, plant tissue or seedhomogenates (optionally surface-sterilized) on antibiotic free media andidentified visually by colony morphotype and molecular methods describedherein. Representative colony morphotypes are also used in colony PCRand sequencing for isolate identification via ribosomal gene sequenceanalysis as described herein. These trials are repeated twice perexperiment, with 5 biological samples per treatment.

XIV. Culture-Independent Methods to Confirm Colonization of the Plant orSeeds by Bacteria or Fungi

One way to detect the presence of endophytes on or within plants orseeds is to use quantitative PCR (qPCR). Internal colonization by theendophyte can be demonstrated by using surface-sterilized plant tissue(including seed) to extract total DNA, and isolate-specific fluorescentMGB probes and amplification primers are used in a qPCR reaction. Anincrease in the product targeted by the reporter probe at each PCR cycletherefore causes a proportional increase in fluorescence due to thebreakdown of the probe and release of the reporter. Fluorescence ismeasured by a quantitative PCR instrument and compared to a standardcurve to estimate the number of fungal or bacterial cells within theplant.

XV. Experimental Description

The design of both species-specific amplification primers, andisolate-specific fluorescent probes are well known in the art. Planttissues (seeds, stems, leaves, flowers, etc.) are pre-rinsed and surfacesterilized using the methods described herein.

Total DNA is extracted using methods known in the art, for example usingcommercially available Plant-DNA extraction kits, or the followingmethod.

Tissue is placed in a cold-resistant container and 10-50 mL of liquidnitrogen is applied. Tissues are then macerated to a powder.

Genomic DNA is extracted from each tissue preparation, following achloroform:isoamyl alcohol 24:1 protocol (Sambrook, Joseph, Edward F.Fritsch, and Thomas Maniatis. Molecular cloning. Vol. 2. New York: Coldspring harbor laboratory press, 1989.).

Quantitative PCR is performed essentially as described by Gao, Zhan, etal. Journal of clinical microbiology 48.10 (2010): 3575-3581 withprimers and probe(s) specific to the desired isolate using aquantitative PCR instrument, and a standard curve is constructed byusing serial dilutions of cloned PCR products corresponding to thespecie-specific PCR amplicon produced by the amplification primers. Dataare analyzed using instructions from the quantitative PCR instrument'smanufacturer software.

As an alternative to qPCR, Terminal Restriction Fragment LengthPolymorphism, (TRFLP) can be performed, essentially as described inJohnston-Monje D, Raizada MN (2011) PLoS ONE 6(6): e20396. Groupspecific, fluorescently labelled primers are used to amplify a subset ofthe microbial population, especially bacteria, especially fungi,especially archaea, especially viruses. This fluorescently labelled PCRproduct is cut by a restriction enzyme chosen for heterogeneousdistribution in the PCR product population. The enzyme cut mixture offluorescently labelled and unlabeled DNA fragments is then submitted forsequence analysis on a Sanger sequence platform such as the AppliedBiosystems 3730 DNA Analyzer.

XVI. Immunological Methods to Detect Microbes in Seeds and VegetativeTissues

A polyclonal antibody is raised against specific bacteria X or fungus Ystrains via standard methods. A polyclonal antibody is also raisedagainst specific GUS and GFP proteins via standard methods.Enzyme-linked immunosorbent assay (ELISA) and immunogold labeling isalso conducted via standard methods, briefly outlined below.

Immunofluorescence microscopy procedures involve the use of semi-thinsections of seed or seedling or adult plant tissues transferred to glassobjective slides and incubated with blocking buffer (20 mM Tris(hydroxymethyl)-aminomethane hydrochloride (TBS) plus 2% bovine serumalbumin, pH 7.4) for 30 min at room temperature. Sections are firstcoated for 30 min with a solution of primary antibodies and then with asolution of secondary antibodies (goat anti-rabbit antibodies) coupledwith fluorescein isothiocyanate (FITC) for 30 min at room temperature.Samples are then kept in the dark to eliminate breakdown of thelight-sensitive FITC. After two 5-min washings with sterile potassiumphosphate buffer (PB) (pH 7.0) and one with double-distilled water,sections are sealed with mounting buffer (100 mL 0.1 M sodium phosphatebuffer (pH 7.6) plus 50 mL double-distilled glycerine) and observedunder a light microscope equipped with ultraviolet light and a FITCTexas-red filter.

Ultra-thin (50- to 70-nm) sections for TEM microscopy are collected onpioloform-coated nickel grids and are labeled with 15-nm gold-labeledgoat anti-rabbit antibody. After being washed, the slides are incubatedfor 1 h in a 1:50 dilution of 5-nm gold-labeled goat anti-rabbitantibody in IGL buffer. The gold labeling is then visualized for lightmicroscopy using a BioCell silver enhancement kit. Toluidine blue(0.01%) is used to lightly counterstain the gold-labeled sections. Inparallel with the sections used for immunogold silver enhancement,serial sections are collected on uncoated slides and stained with 1%toluidine blue. The sections for light microscopy are viewed under anoptical microscope, and the ultrathin sections are viewed by TEM.

XVII. Characterization of Uniformity of Endophytes in a Population ofSeeds

To test for the homogeneity of endophytes either on the surface orcolonizing the interior tissues in a population of seeds, seeds aretested for the presence of the microbes by culture-dependent and/or-independent methods. Seeds are obtained, surface sterilized andpulverized, and the seed homogenate is divided and used to inoculateculture media or to extract DNA and perform quantitative PCR. Thehomogeneity of colonization in a population of seeds is assessed throughdetection of specific microbial strains via these methods and comparisonof the culture-dependent and culture-independent results across thepopulation of seeds. Homogeneity of colonization for a strain ofinterest is rated based on the total number of seeds in a populationthat contain a detectable level of the strain, on the uniformity acrossthe population of the number of cells or CFU of the strain present inthe seed, or based on the absence or presence of other microbial strainsin the seed.

XVIII. Experimental Description

Surface sterilized seeds are obtained as described herein. Forculture-dependent methods of microbial-presence confirmation, bacterialand fungi are obtained from seeds essentially as described herein withthe following modification. Seed homogenate is used to inoculate mediacontaining selective and/or differential additives that will allow toidentification of a particular microbe.

For qPCR, total DNA of each seed is extracted using methods known in theart, as described herein.

XIX. Characterization of Homogeneity of Colonization in Population ofPlants

To test for the homogeneity of microorganisms (including endophytes)colonizing the interior in a population of plants, tissues from eachplant are tested for the presence of the microbes by culture-dependentand/or -independent methods. Tissues are obtained, surface sterilizedand pulverized, and the tissue material is divided and used to inoculateculture media or to extract DNA and perform quantitative PCR. Thehomogeneity of colonization in a population of plants is assessedthrough detection of specific microbial strains via these methods andcomparison of the culture-dependent and culture-independent resultsacross the population of plants or their tissues. Homogeneity ofcolonization for a strain of interest is rated based on the total numberof plants in a population that contain a detectable level of the strain,on the uniformity across the population of the number of cells or CFU ofthe strain present in the plant tissue, or based on the absence orpresence of other microbial strains in the plant.

XX. Experimental Description

Surface sterilized plant tissues are obtained as described herein. Forculture-dependent methods of microbial-presence confirmation, bacterialand fungi are obtained from plant tissues essentially as describedherein with the following modification. Plant tissue homogenate is usedto inoculate media containing selective and/or differential additivesthat will allow identification of a particular microbe.

For qPCR, total DNA of each plant tissue is extracted using methodsknown in the art, as described herein.

Other embodiments will be apparent to those skilled in the art fromconsideration of the specification and practice of the embodiments.Consider the specification and examples as exemplary only, with a truescope and spirit being indicated by the following claims.

1. (canceled)
 2. (canceled)
 3. A method for preparing a seed comprisingan endophyte population, said method comprising applying to an exteriorsurface of a seed a formulation comprising an endophyte populationconsisting essentially of an endophyte comprising a 16S rRNA or ITS rRNAnucleic acid sequence at least 95% identical to a nucleic acid sequenceselected from the group consisting of SEQ ID NOs: 1-455. 4.-7.(canceled)
 8. The method of claim 3, wherein the endophyte is capable ofa function or activity selected from the group consisting of auxinproduction, nitrogen fixation, production of an antimicrobial compound,mineral phosphate solubilization, siderophore production, cellulaseproduction, chitinase production, xylanase production, and acetoinproduction.
 9. The method of claim 8, wherein the endophyte exhibits atleast two of: auxin production, nitrogen fixation, production of anantimicrobial compound, mineral phosphate solubilization, siderophoreproduction, cellulase production, chitinase production, xylanaseproduction, and acetoin production.
 10. The method of claim 3, whereinthe endophyte is capable of metabolizing at least one substrate selectedfrom the group consisting of: a-D-glucose, arabinose, arbutin,b-methyl-D-galactoside, b-methyl-D-glucoside, D-alanine, D-arabitol,D-aspartic acid, D-cellobiose, dextrin, D-fructose, D-galactose,D-gluconic acid, D-glucosamine, dihydroxyacetone, DL-malic acid,D-mannitol, D-mannose, D-melezitose, D-melibiose, D-raffinose, D-ribose,D-serine, D-threonine, D-trehalose, D-xylose, g-amino-N-butyric acid,g-cyclodextrin, gelatin, gentiobiose, glycogen, glycyl-L-aspartic acid,glycyl-L-glutamic acid, glycyl-L-proline, glyoxylic acid, i-erythritol,inosine, L-alanine, L-alanyl-glycine, L-arabinose, L-asparagine,L-aspartic acid, L-galactonic acid-g-lactone, L-glutamic acid,L-glutamine, L-histidine, L-proline, L-rhamnose, L-serine, L-threonine,maltitol, maltose, maltotriose, mannose, N-acetyl-D-glucosamine, oxalicacid, palatinose, pectin, proline, salicin, stachyose, sucrose,trehalose, turanose, tyramine, uridine, and xylose.
 11. The method ofclaim 3, wherein the endophyte is capable of metabolizing at least twosubstrates selected from the group consisting of: a-D-glucose,arabinose, arbutin, b-methyl-D-galactoside, b-methyl-D-glucoside,D-alanine, D-arabitol, D-aspartic acid, D-cellobiose, dextrin,D-fructose, D-galactose, D-gluconic acid, D-glucosamine,dihydroxyacetone, DL-malic acid, D-mannitol, D-mannose, D-melezitose,D-melibiose, D-raffinose, D-ribose, D-serine, D-threonine, D-trehalose,D-xylose, g-amino-N-butyric acid, g-cyclodextrin, gelatin, gentiobiose,glycogen, glycyl-L-aspartic acid, glycyl-L-glutamic acid,glycyl-L-proline, glyoxylic acid, i-erythritol, inosine, L-alanine,L-alanyl-glycine, L-arabinose, L-asparagine, L-aspartic acid,L-galactonic acid-g-lactone, L-glutamic acid, L-glutamine, L-histidine,L-proline, L-rhamnose, L-serine, L-threonine, maltitol, maltose,maltotriose, mannose, N-acetyl-D-glucosamine, oxalic acid, palatinose,pectin, proline, salicin, stachyose, sucrose, trehalose, turanose,tyramine, uridine, and xylose.
 12. The method of claim 3, wherein theendophyte is present at a concentration of at least 10² CFU or sporesper seed on the surface of seeds after contacting.
 13. The method ofclaim 3, wherein the applying or contacting comprises spraying,immersing, coating, encapsulating, or dusting the seeds or seedlingswith the formulation.
 14. The method of claim 3, wherein the benefit oragricultural trait is selected from the group consisting of: increasedroot biomass, increased root length, increased height, increased shootlength, increased leaf number, increased water use efficiency, increasedtolerance to low nitrogen stress, increased nitrogen use efficiency,increased overall biomass, increased grain yield, increasedphotosynthesis rate, increased tolerance to drought, increased heattolerance, increased salt tolerance, increased resistance to nematodestress, increased resistance to a fungal pathogen, increased resistanceto a bacterial pathogen, increased resistance to a viral pathogen, adetectable modulation in the level of a metabolite, a detectablemodulation in the transcriptome, and a detectable modulation in theproteome, relative to reference seeds or agricultural plants derivedfrom reference seeds.
 15. (canceled)
 16. (canceled)
 17. The method ofclaim 3, wherein the formulation comprises at least one member selectedfrom the group consisting of an agriculturally compatible carrier, atackifier, a microbial stabilizer, a fungicide, an antibacterial agent,an herbicide, a nematicide, an insecticide, a plant growth regulator, arodenticide, and a nutrient. 18.-86. (canceled)
 87. An agriculturalformulation comprising an endophyte comprising a nucleic acid sequencethat is at least 97% identical, at least 98% identical, at least 99%identical, at least 99.5% identical, or 100% identical, to a nucleicacid sequence selected from the group consisting of SEQ ID NOs: 1-455that is present in an amount effective to colonize a mature agriculturalplant, wherein the formulation further comprises at least one memberselected from the group consisting of an agriculturally compatiblecarrier, a tackifier, a microbial stabilizer, a fungicide, anantibacterial agent, an herbicide, a nematicide, an insecticide, a plantgrowth regulator, a rodenticide, and a nutrient.
 88. The formulation ofclaim 87, wherein the agricultural plant is a monocot.
 89. Theformulation of claim 88, wherein the agricultural plant is selected fromthe group consisting of maize, barley, rice and wheat.
 90. Theformulation of claim 87, wherein the agricultural plant is a dicot. 91.The formulation of claim 90, wherein the agricultural plant is selectedfrom the group consisting of soybean, canola, cotton, Brassica Napus,tomato, squash, cucumber, pepper, peanut, sunflower, and sugar beet. 92.The formulation of claim 87, wherein the population consists essentiallyof an endophyte comprising a nucleic acid sequence that is at least 99%identical to a nucleic acid sequence selected from the group consistingof SEQ ID NOs: 1-455.
 93. The formulation of claim 87, wherein thepopulation consists essentially of an endophyte comprising a nucleicacid sequence that is at least 99.5% identical to a nucleic acidsequence selected from the group consisting of SEQ ID NOs: 1-455. 94.The formulation of claim 87, comprising at least two differentendophytes each comprise a nucleic acid sequence that is at least 97%identical, at least 98% identical, at least 99% identical, at least99.5% identical, or 100% identical, to a nucleic acid sequence selectedfrom the group consisting of SEQ ID NOs: 1-455. 95.-107. (canceled) 108.A synthetic combination comprising at least two endophytes associatedwith a seed, wherein at least the first endophyte is heterologous to theseed and wherein the first endophyte comprises a 16S rRNA or ITS rRNAnucleic acid sequence at least 97% identical to a nucleic acid sequenceselected from the group consisting of SEQ ID NOs: 1-455, wherein theendophytes are present in the formulation in an amount effective toprovide a benefit to the seeds or seedlings or the plants derived fromthe seeds or seedlings.
 109. The synthetic combination of claim 108,wherein the first endophyte is capable of metabolizing at least onesubstrate selected from the group of: a-D-glucose, arabinose, arbutin,b-methyl-D-galactoside, b-methyl-D-glucoside, D-alanine, D-arabitol,D-aspartic acid, D-cellobiose, dextrin, D-fructose, D-galactose,D-gluconic acid, D-glucosamine, dihydroxyacetone, DL-malic acid,D-mannitol, D-mannose, D-melezitose, D-melibiose, D-raffinose, D-ribose,D-serine, D-threonine, D-trehalose, D-xylose, g-amino-N-butyric acid,g-cyclodextrin, gelatin, gentiobiose, glycogen, glycyl-L-aspartic acid,glycyl-L-glutamic acid, glycyl-L-proline, glyoxylic acid, i-erythritol,inosine, L-alanine, L-alanyl-glycine, L-arabinose, L-asparagine,L-aspartic acid, L-galactonic acid-g-lactone, L-glutamic acid,L-glutamine, L-histidine, L-proline, L-rhamnose, L-serine, L-threonine,maltitol, maltose, maltotriose, mannose, N-acetyl-D-glucosamine, oxalicacid, palatinose, pectin, proline, salicin, stachyose, sucrose,trehalose, turanose, tyramine, uridine, and xylose. 110.-228. (canceled)